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    Author Title Year Journal / Proceedings / Book Reftype
    Radauer-Preiml, I., Andosch, A., Hawranek, T., Luetz-Meindl, U., Wiederstein, M., Horejs-Hoeck, J., Himly, M., Boyles, M. & Duschl, A. Nanoparticle-allergen interactions mediate human allergic responses: protein corona characterization and cellular responses. 2016 Part Fibre Toxicol
    Vol. 13(3), pp. 1--15 
    article DOI URL 
    Abstract: Engineered nanomaterials (ENMs) interact with different biomolecules as soon as they are in contact, resulting in the formation of a biomolecule 'corona'. Hence, the 'corona' defines the biological identity of the ENMs and could affect the response of the immune system to ENM exposure. With up to 40 \% of the world population suffering from type I allergy, a possible modulation of allergen effects by binding to ENMs is highly relevant with respect to work place and consumer safety. Therefore, the aim of this present study was to gain an insight into the interactions of gold nanoparticles with different seasonally and perennially occurring outdoor and indoor allergens.Gold nanoparticles (AuNPs) were conjugated with the major allergens of birch pollen (Bet v 1), timothy grass pollen (Phl p 5) and house dust mite (Der p 1). The AuNP-allergen conjugates were characterized by means of TEM negative staining, dynamic light scattering (DLS), z-potential measurements and hyperspectral imaging. Furthermore, 3D models were constructed, based on the characterization data, to visualize the interaction between the allergens and the AuNPs surface. Differences in the activation of human basophil cells derived from birch/grass pollen- and house dust mite-allergic patients in response to free allergen and AuNP-allergen conjugates were determined using the basophil activation assay (BAT). Potential allergen corona replacement during BAT was controlled for using Western blotting. The protease activity of AuNP-Der p 1 conjugates compared to free Der p 1 was assessed, by an enzymatic activity assay and a cellular assay pertaining to lung type II alveolar epithelial cell tight junction integrity.The formation of a stable corona was found for all three allergens used. Our data suggest, that depending on the allergen, different effects are observed after binding to ENMs, including enhanced allergic responses against Der p 1 and also, for some patients, against Bet v 1. Moreover elevated protease activity of AuNP-Der p 1 conjugates compared to free Der p 1 was found. In summary, this study presents that conjugation of allergens to ENMs can modulate the human allergic response, and that protease activity can be increased.
    BibTeX:
    @Article{Radauer-Preiml.Andosch.ea-2016,
      Title                    = {Nanoparticle-allergen interactions mediate human allergic responses: protein corona characterization and cellular responses.},
      Author                   = {Radauer-Preiml, Isabella and Andosch, Ancuela and Hawranek, Thomas and Luetz-Meindl, Ursula and Wiederstein, Markus and Horejs-Hoeck, Jutta and Himly, Martin and Boyles, Matthew and Duschl, Albert},
      Journal                  = {Part Fibre Toxicol},
      Year                     = {2016},
      Volume                   = {13},
      Pages                    = {1--15},
      Doi                      = {10.1186/s12989-016-0113-0},
      Url                      = {http://dx.doi.org/10.1186/s12989-016-0113-0}
    }
    
    Espada, R., Parra, R.G., Sippl, M.J., Mora, T., Walczak, A. & Ferreiro, D.U. Repeat proteins challenge the concept of structural domains. 2015 Biochem Soc Trans
    Vol. 43(5), pp. 844--849 
    article DOI URL 
    Abstract: Structural domains are believed to be modules within proteins that can fold and function independently. Some proteins show tandem repetitions of apparent modular structure that do not fold independently, but rather co-operate in stabilizing structural forms that comprise several repeat-units. For many natural repeat-proteins, it has been shown that weak energetic links between repeats lead to the breakdown of co-operativity and the appearance of folding sub-domains within an apparently regular repeat array. The quasi-1D architecture of repeat-proteins is crucial in detailing how the local energetic balances can modulate the folding dynamics of these proteins, which can be related to the physiological behaviour of these ubiquitous biological systems.
    BibTeX:
    @Article{Espada.Parra.ea-2015,
      Title                    = {Repeat proteins challenge the concept of structural domains.},
      Author                   = {Espada, Roc{\'{\i}}o and Parra, R Gonzalo and Sippl, Manfred J. and Mora, Thierry and Walczak, Aleksandra M. and Ferreiro, Diego U.},
      Journal                  = {Biochem Soc Trans},
      Year                     = {2015},
      Volume                   = {43},
      Pages                    = {844--849},
      Doi                      = {10.1042/BST20150083},
      Url                      = {http://dx.doi.org/10.1042/BST20150083}
    }
    
    Wiederstein, M., Gruber, M., Frank, K., Melo, F. & Sippl, M.J. Structure-based characterization of multiprotein complexes. 2014 Structure
    Vol. 22(7), pp. 1063-1070 
    article DOI URL 
    Abstract: Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies.
    BibTeX:
    @article{Wiederstein.Gruber.ea-2014,
      author = {Markus Wiederstein and Markus Gruber and Karl Frank and Francisco
    	Melo and Manfred J Sippl},
      title = {Structure-Based Characterization of Multiprotein Complexes.},
      journal = {Structure},
      year = {2014},
      volume = {22},
      pages = {1063--1070},
      doi = {10.1016/j.str.2014.05.005},
      url = {http://dx.doi.org/10.1016/j.str.2014.05.005}
    }
    
    Parra, R.G., Espada, R., Sanchez, I.E., Sippl, M.J. & Ferreiro, D.U. Detecting repetitions and periodicities in proteins by tiling the structural space. 2013 J Phys Chem B
    Vol. 117(42), pp. 12887-12897 
    article DOI URL 
    Abstract: The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy landscape theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal Frustration" when the folded structure is symmetric (Wolynes, P. G. Symmetry and the Energy Landscapes of Biomolecules. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 14249-14255). Similarly, repeats and structural mosaics may be fundamentally related to landscapes with multiple embedded funnels. Here we present analytical tools to detect and compare structural repetitions in protein molecules. By an exhaustive analysis of the distribution of structural repeats using a robust metric, we define those portions of a protein molecule that best describe the overall structure as a tessellation of basic units. The patterns produced by such tessellations provide intuitive representations of the repeating regions and their association toward higher order arrangements. We find that some protein architectures can be described as nearly periodic, while in others clear separations between repetitions exist. Since the method is independent of amino acid sequence information, we can identify structural units that can be encoded by a variety of distinct amino acid sequences.
    BibTeX:
    @article{Parra.Espada.ea-2013,
      author = {R. Gonzalo Parra and Rocío Espada and Ignacio E Sanchez and Manfred J Sippl and Diego U Ferreiro},
      title = {Detecting repetitions and periodicities in proteins by tiling the structural space.},
      journal = {J Phys Chem B},
      year = {2013},
      volume = {117},
      number = {42},
      pages = {12887--12897},
      url = {http://dx.doi.org/10.1021/jp402105j},
      doi = {http://dx.doi.org/10.1021/jp402105j}
    }
    
    Slater, A.W., Castellanos, J.I., Sippl, M.J. & Melo, F. Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments. 2013 Bioinformatics
    Vol. 29, pp. 47-53 
    article DOI URL 
    Abstract: MOTIVATION: Pairwise alignment of protein structures is a fundamental task in structural bioinformatics. There are numerous computer programs in the public domain that produce alignments for a given pair of protein structures but the results obtained by the various programs generally differ substantially. Hence, in the application of such programs the question arises which of the alignment programs are the most trustworthy in the sense of overall performance, and which programs provide the best result for a given pair of proteins. The major problem in comparing, evaluating, and judging alignment results is that there is no clear notion of the optimality of an alignment. As a consequence, the numeric criteria and scores reported by the individual structure alignment programs are largely incomparable. RESULTS: Here we report on the development and application of a new approach for the evaluation of structure alignment results. The method uses the translation vector and rotation matrix to generate the superposition of two structures but discards the alignment reported by the individual programs. The optimal alignment is then generated in standardized form based on a suitably implemented dynamic programming algorithm where the length of the alignment is the single most informative parameter. We demonstrate that some of the most popular programs in protein structure research differ considerably in their overall performance. In particular, each of the programs investigated here produced in at least in one case the best and the worst alignment compared to all others. Hence, at the current state of development of structure comparison techniques, it is advisable to use several programs in parallel and to choose the optimal alignment in the way reported here. AVAILABILITY: The computer software that implement the method described here is freely available at http://melolab.org/stovcahttp://melolab.org/stovca CONTACT: fmelo@bio.puc.cl.
    BibTeX:
    @article{Slater.Castellanos.ea-2012,
      author = {Alex W Slater and Javier I Castellanos and Manfred J Sippl and Francisco Melo},
      title = {Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments.},
      journal = {Bioinformatics},
      year = {2013},
      volume = {29},
      pages = {47-53},
      url = {http://dx.doi.org/10.1093/bioinformatics/bts600},
      doi = {http://dx.doi.org/10.1093/bioinformatics/bts600}
    }
    
    Bach, D., Fuereder, J., Karbiener, M., Scheideler, M., Ress, A.L., Neureiter, D., Kemmerling, R., Dietze, O., Wiederstein, M., Berr, F., Plaetzer, K., Kiesslich, T. & Martin Pichler Comprehensive analysis of alterations in the miRNome in response to photodynamic treatment. 2013 J Photochem Photobiol B
    Vol. 120, pp. 74-81 
    article DOI URL 
    Abstract: Photodynamic therapy (PDT) is a local tumour treatment accepted for a number of indications. PDT operates via the cellular stress response through the production of reactive oxygen species and subsequent cellular damage, resulting in cell death. Although PDT-induced signalling and cytotoxicity mechanisms have been investigated, the effect of PDT on microRNA (miRNA) expression is largely unknown. Therefore, we conducted a comprehensive microarray-based analysis of the miRNome of human epidermoid carcinoma cells (A431) following in vitro photodynamic treatment using polyvinylpyrrolidone hypericin (PVPH) as a photosensitiser and nearly homogeneous apoptosis-inducing conditions. Using microarray analysis we found eight miRNAs to be significantly differentially expressed 5h post treatment compared with the baseline levels and three miRNAs with more than 2-fold differential expression that could be detected in 1 or 2 biological replicates. The verification of these results by quantitative RT-PCR including a detailed time-course revealed an up to 15-fold transient over-expression of miR-634, miR-1246, miR-1290 and miR-487b compared with the basal level. For these miRNAs, in silico mRNA target prediction yielded numerous target transcripts involved in the regulation of cell stress, apoptosis, cell adherence and proliferation. This study provides the first comprehensive miRNome analysis after PDT treatment and may help to develop novel miRNA-based therapeutic approaches to further increase the efficiency of PDT.
    BibTeX:
    @article{Bach.Fuereder.ea-2013,
      Title                    = {Comprehensive analysis of alterations in the miRNome in response to photodynamic treatment.},
      Author                   = {Doris Bach and Julia Fuereder and Michael Karbiener and Marcel Scheideler and Anna Lena Ress and Daniel Neureiter and Ralf Kemmerling and Otto Dietze and Markus Wiederstein and Frieder Berr and Kristjan Plaetzer and Tobias Kiesslich and Martin Pichler},
      Journal                  = {J Photochem Photobiol B},
      Year                     = {2013},
      Pages                    = {74--81},
      Volume                   = {120},
      Doi                      = {10.1016/j.jphotobiol.2013.01.012},
      Url                      = {http://dx.doi.org/10.1016/j.jphotobiol.2013.01.012}
    }
    
    Sippl, M.J. & Wiederstein, M. Detection of spatial correlations in protein structures and molecular complexes. 2012 Structure
    Vol. 20, pp. 718-728 
    article DOI URL 
    Abstract: Protein structures are frequently related by spectacular and often surprising similarities. Structural correlations among protein chains are routinely detected by various structure-matching techniques, but the comparison of oligomers and molecular complexes is largely uncharted territory. Here we solve the structure-matching problem for oligomers and large molecular aggregates, including the largest molecular complexes known today. We provide several challenging examples that cannot be handled by conventional structure-matching techniques and we report on a number of remarkable correlations. The examples cover the cell-puncturing device of bacteriophage T4, the secretion system of P. aeruginosa, members of the dehydrogenase family, DNA clamps, ferredoxin iron-storage cages, and virus capsids.
    BibTeX:
    @ARTICLE{Sippl.Wiederstein-2012,
      author = {Manfred J Sippl and Markus Wiederstein},
      title = {Detection of spatial correlations in protein structures and molecular
    	complexes.},
      journal = {Structure},
      year = {2012},
      volume = {20},
      pages = {718--728},
      doi = {10.1016/j.str.2012.01.024},
      url = {http://dx.doi.org/10.1016/j.str.2012.01.024}
    }
    
    Suhrer, S.J., Gruber, M., Wiederstein, M. & Sippl, M.J. Effective techniques for protein structure mining. 2012 Methods Mol Biol
    Vol. 857, pp. 33-54 
    article DOI URL 
    Abstract: Retrieval and characterization of protein structure relationships are instrumental in a wide range of tasks in structural biology. The classification of protein structures (COPS) is a web service that provides efficient access to structure and sequence similarities for all currently available protein structures. Here, we focus on the application of COPS to the problem of template selection in homology modeling.
    BibTeX:
    @article{Suhrer.Gruber.ea-2012,
      author = {Stefan J Suhrer and Markus Gruber and Markus Wiederstein and Manfred J Sippl},
      title = {Effective techniques for protein structure mining.},
      journal = {Methods Mol Biol},
      year = {2012},
      volume = {857},
      pages = {33--54},
      url = {http://dx.doi.org/10.1007/978-1-61779-588-6_2},
      doi = {http://dx.doi.org/10.1007/978-1-61779-588-6_2}
    }
    
    Ginzinger, S.W., Gruber, M., Brandstetter, H. & Sippl, M.J. Real space refinement of crystal structures with canonical distributions of electrons. 2011 Structure
    Vol. 19(12), pp. 1739-1743 
    article DOI URL 
    Abstract: Recurring groups of atoms in molecules are surrounded by specific canonical distributions of electrons. Deviations from these distributions reveal unrealistic molecular geometries. Here, we show how canonical electron densities can be combined with classical electron densities derived from X-ray diffraction experiments to drive the real space refinement of crystal structures. The refinement process generally yields superior molecular models with reduced excess electron densities and improved stereochemistry without compromising the agreement between molecular models and experimental data.
    BibTeX:
    @article{Ginzinger.Gruber.ea-2011,
      author = {Simon W Ginzinger and Markus Gruber and Hans Brandstetter and Manfred J Sippl},
      title = {Real space refinement of crystal structures with canonical distributions of electrons.},
      journal = {Structure},
      year = {2011},
      volume = {19},
      number = {12},
      pages = {1739--1743},
      url = {http://dx.doi.org/10.1016/j.str.2011.10.011},
      doi = {http://dx.doi.org/10.1016/j.str.2011.10.011}
    }
    
    Han, B., Liu, Y., Ginzinger, S.W. & Wishart, D.S. SHIFTX2: significantly improved protein chemical shift prediction. 2011 J Biomol NMR
    Vol. 50, pp. 43-57 
    article DOI URL 
    Abstract: A new computer program, called SHIFTX2, is described which is capable of rapidly and accurately calculating diamagnetic (1)H, (13)C and (15)N chemical shifts from protein coordinate data. Compared to its predecessor (SHIFTX) and to other existing protein chemical shift prediction programs, SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3× smaller) than the next best performing program. It also provides significantly more coverage (up to 10% more), is significantly faster (up to 8.5×) and capable of calculating a wider variety of backbone and side chain chemical shifts (up to 6×) than many other shift predictors. In particular, SHIFTX2 is able to attain correlation coefficients between experimentally observed and predicted backbone chemical shifts of 0.9800 ((15)N), 0.9959 ((13)C?), 0.9992 ((13)C?), 0.9676 ((13)C'), 0.9714 ((1)HN), 0.9744 ((1)H?) and RMS errors of 1.1169, 0.4412, 0.5163, 0.5330, 0.1711, and 0.1231 ppm, respectively. The correlation between SHIFTX2's predicted and observed side chain chemical shifts is 0.9787 ((13)C) and 0.9482 ((1)H) with RMS errors of 0.9754 and 0.1723 ppm, respectively. SHIFTX2 is able to achieve such a high level of accuracy by using a large, high quality database of training proteins (>190), by utilizing advanced machine learning techniques, by incorporating many more features (?(2) and ?(3) angles, solvent accessibility, H-bond geometry, pH, temperature), and by combining sequence-based with structure-based chemical shift prediction techniques. With this substantial improvement in accuracy we believe that SHIFTX2 will open the door to many long-anticipated applications of chemical shift prediction to protein structure determination, refinement and validation. SHIFTX2 is available both as a standalone program and as a web server ( http://www.shiftx2.ca ).
    BibTeX:
    @article{Han2011,
      author = {Beomsoo Han and Yifeng Liu and Simon W Ginzinger and David S Wishart},
      title = {SHIFTX2: significantly improved protein chemical shift prediction.},
      journal = {J Biomol NMR},
      volume = {50},
      pages = {43--57},
      year = {2011},
      url = {http://dx.doi.org/10.1007/s10858-011-9478-4},
      doi = {http://dx.doi.org/10.1007/s10858-011-9478-4}
    }
    
    Ginzinger, S.W.; Weichenberger, C.X. & Sippl, M.J. Detection of unrealistic molecular environments in protein structures based on expected electron densities. 2010 J Biomol NMR
    Vol. 47 (1) , pp. 33-40  
    article
    Abstract: Understanding the relationship between protein structure and biological function is a central theme in structural biology. Advances are severely hampered by errors in experimentally determined protein structures. Detection and correction of such errors is therefore of utmost importance. Electron densities in molecular structures obey certain rules which depend on the molecular environment. Here we present and discuss a new approach that relates electron densities computed from a structural model to densities expected from prior observations on identical or closely related molecular environments. Strong deviations of computed from expected densities reveal unrealistic molecular structures. Most importantly, structure analysis and error detection are independent of experimental data and hence may be applied to any structural model. The comparison to state-of-the-art methods reveals that our approach is able to identify errors that formerly remained undetected. The new technique, called RefDens, is accessible as a public web service at http://refdens.services.came.sbg.ac.at.
    BibTeX:
    @article{Ginzinger.Weichenberger.ea-2010,
      author = {Simon W Ginzinger and Christian X Weichenberger and Manfred J Sippl},
      title = {Detection of unrealistic molecular environments in protein structures based on expected electron densities.},
      journal = {J Biomol NMR},
      year = {2010},
      volume = {47},
      number = {1},
      pages = {33--40},
      url = {http://dx.doi.org/10.1007/s10858-010-9408-x},
      doi = {http://dx.doi.org/10.1007/s10858-010-9408-x}
    }
    					
    Frank, K.; Gruber, M. & Sippl, M.J. COPS Benchmark: interactive analysis of database search methods. 2010 Bioinformatics
    Vol. 26 (4) , pp. 574-575  
    article
    Abstract: SUMMARY: The performance of sequence database search methods is usually judged by receiver operating characteristic (ROC) analysis. The proper interpretation of the results obtained and a fair comparison across different methods critically depends on the properties of the data set used for such an analysis; in particular, each query must have the same number of true positives and true negatives. Here, we present a novel web service based on a dataset specifically designed for ROC analysis and the investigation of alignment quality. The data set is derived from a quantitative classification of protein structures (COPS), while analysis and results are presented through an intuitive web interface. The analysis provides details such as false positives per query, and visualization of the structural similarity between query and targets. Most importantly, results obtained for a specific alignment method are immediately related to those obtained for several popular standard sequence alignment methods. AVAILABILITY: The COPS-Benchmark service is available at http://benchmark.services.came.sbg.ac.at CONTACT: publications@came.sbg.ac.at.
    BibTeX:
    @article{Frank.Gruber.ea-2010,
      author = {Karl Frank and Markus Gruber and Manfred J Sippl},
      title = {COPS Benchmark: interactive analysis of database search methods.},
      journal = {Bioinformatics},
      year = {2010},
      volume = {26},
      number = {4},
      pages = {574--575},
      url = {http://dx.doi.org/10.1093/bioinformatics/btp712},
      doi = {http://dx.doi.org/10.1093/bioinformatics/btp712}
    }
    					
    Suhrer, S.J.; Wiederstein, M.; Gruber, M. & Sippl, M.J. COPS-a novel workbench for explorations in fold space. 2009 Nucleic Acids Res
    Vol. 37 (Web Server issue) , pp. W539-W544  
    article
    Abstract: The COPS (Classification Of Protein Structures) web server provides access to the complete repertoire of known protein structures and protein structural domains. The COPS classification encodes pairwise structural similarities as quantified metric relationships. The resulting metrical structure is mapped to a hierarchical tree, which is largely equivalent to the structure of a file browser. Exploiting this relationship we implemented the Fold Space Navigator, a tool that makes navigation in fold space as convenient as browsing through a file system. Moreover, pairwise structural similarities among the domains can be visualized and inspected instantaneously. COPS is updated weekly and stays concurrent with the PDB repository. The server also exposes the COPS classification pipeline. Newly determined structures uploaded to the server are chopped into domains, the locations of the new domains in the classification tree are determined, and their neighborhood can be immediately explored through the Fold Space Navigator. The COPS web server is accessible at http://cops.services.came.sbg.ac.at/.
    BibTeX:
    @article{Suhrer.Wiederstein.ea-2009,
      author = {Stefan J Suhrer and Markus Wiederstein and Markus Gruber and Manfred J Sippl},
      title = {COPS--a novel workbench for explorations in fold space.},
      journal = {Nucleic Acids Res},
      year = {2009},
      volume = {37},
      number = {Web Server issue},
      pages = {W539--W544},
      url = {http://dx.doi.org/10.1093/nar/gkp411},
      doi = {http://dx.doi.org/10.1093/nar/gkp411}
    }
    					
    Sippl, M.J. Fold space unlimited. 2009 Curr Opin Struct Biol
    Vol. 19 (3) , pp. 312-320  
    article
    Abstract: You want to know how proteins do it? Take a walk in protein fold space. More often than not you will get a clue if not the answer. If you know what you are looking for and how to find it. In fact, there is more information than we can presently handle. Charting fold space and chasing its creatures has occupied us for the past decades. There is no end in sight.
    BibTeX:
    @article{Sippl-2009,
      author = {Manfred J Sippl},
      title = {Fold space unlimited.},
      journal = {Curr Opin Struct Biol},
      year = {2009},
      volume = {19},
      number = {3},
      pages = {312--320},
      url = {http://dx.doi.org/10.1016/j.sbi.2009.03.010},
      doi = {http://dx.doi.org/10.1016/j.sbi.2009.03.010}
    }
    					
    Weichenberger, C.X.; Byzia, P. & Sippl, M.J. Visualization of unfavorable interactions in protein folds. 2008 Bioinformatics
    Vol. 24 (9) , pp. 1206-1207  
    article
    Abstract: Three dimensional structures of proteins contain errors which often originate from limitations of the experimental techniques employed. Such errors frequently result in unfavorable atomic interactions. Here we present a new web service, called Interaction Viewer, for the visualization and correction of such errors. We show how the Interaction Viewer is used in combination with the NQ-Flipper service to spot strained asparagine and glutamine rotamers and we emphasize the convenience of this service in correcting such errors. AVAILABILITY: The web service is integrated with the NQ-Flipper service and accessible at http://flipper.services.came.sbg.ac.at
    BibTeX:
    @article{Weichenberger.Byzia.ea-2008a,
      author = {Christian X Weichenberger and Piotr Byzia and Manfred J Sippl},
      title = {Visualization of unfavorable interactions in protein folds.},
      journal = {Bioinformatics},
      year = {2008},
      volume = {24},
      number = {9},
      pages = {1206--1207},
      url = {http://dx.doi.org/10.1093/bioinformatics/btn108},
      doi = {http://dx.doi.org/10.1093/bioinformatics/btn108}
    }
    					
    Sippl, M.J. & Wiederstein, M. A note on difficult structure alignment problems. 2008 Bioinformatics
    Vol. 24 (3) , pp. 426-427  
    article
    Abstract: SUMMARY: Progress in structural biology depends on several key technologies. In particular tools for alignment and superposition of protein structures are indispensable. Here we describe the use of the TopMatch web service, an effective computational tool for protein structure alignment, for the visualization of structural similarities, and for highlighting relationships found in protein classifications. We provide several instructive examples. AVAILABILITY: TopMatch is available as a public web service at http://services.came.sbg.ac.at CONTACT: sippl@came.sbg.ac.at.
    BibTeX:
    @article{Sippl.Wiederstein-2008,
      author = {Manfred J Sippl and Markus Wiederstein},
      title = {A note on difficult structure alignment problems.},
      journal = {Bioinformatics},
      year = {2008},
      volume = {24},
      number = {3},
      pages = {426--427},
      url = {http://dx.doi.org/10.1093/bioinformatics/btm622},
      doi = {http://dx.doi.org/10.1093/bioinformatics/btm622}
    }
    					
    Sippl, M.J.; Suhrer, S.J.; Gruber, M. & Wiederstein, M. A discrete view on fold space. 2008 Bioinformatics
    Vol. 24 (6) , pp. 870-871  
    article
    Abstract: The database of known protein structures contains an overwhelming number of structural similarities that frequently point to intriguing biological relationships. The similarities are often difficult to spot, and once detected their comprehension needs proper visualization. Here we introduce the new concept of a Fold Space Navigator, a user interface enabling the efficient navigation through fold space and the instantaneous visualization of pairwise structure similarities. AVAILABILITY: The Fold Space Navigator is accessible as a public web service at http://services.came.sbg.ac.at
    BibTeX:
    @article{Sippl.Suhrer.ea-2008,
      author = {Manfred J Sippl and Stefan J Suhrer and Markus Gruber and Markus Wiederstein},
      title = {A discrete view on fold space.},
      journal = {Bioinformatics},
      year = {2008},
      volume = {24},
      number = {6},
      pages = {870--871},
      url = {http://dx.doi.org/10.1093/bioinformatics/btn020},
      doi = {http://dx.doi.org/10.1093/bioinformatics/btn020}
    }
    					
    Sippl, M.J.; Suhrer, S.J.; Gruber, M.; Weichenberger, C.X. & Wiederstein, M. Instant Classification of New Protein Structures 2008 Bioinformatics , pp. submitted   article
    BibTeX:
    @article{Sippl.Suhrer.ea-2008b,
      author = {Manfred J Sippl and Stefan J Suhrer and Markus Gruber and Christian X. Weichenberger and Markus Wiederstein},
      title = {Instant Classification of New Protein Structures},
      journal = {Bioinformatics},
      year = {2008},
      pages = {submitted}
    }
    					
    Sippl, M.J.; Suhrer, S.J.; Gruber, M.; Weichenberger, C.X. & Wiederstein, M. On Novelty and Redundancy in Fold Space 2008 Bioinformatics , pp. submitted   article
    BibTeX:
    @article{Sippl.Suhrer.ea-2008a,
      author = {Manfred J Sippl and Stefan J Suhrer and Markus Gruber and Christian X. Weichenberger and Markus Wiederstein},
      title = {On Novelty and Redundancy in Fold Space},
      journal = {Bioinformatics},
      year = {2008},
      pages = {submitted}
    }
    					
    Sippl, M.J. On distance and similarity in fold space. 2008 Bioinformatics
    Vol. 24 (6) , pp. 872-873  
    article
    Abstract: Metric information on similarities and distances in fold space is essential for quantitative work in structural bioinformatics and structural biology. Here we derive a suitable metric for protein structures from the fundamental axioms of similarity. Derivation of the metric also clarifies the relationship between the interrelated concepts of distance and similarity.
    BibTeX:
    @article{Sippl-2008,
      author = {Manfred J Sippl},
      title = {On distance and similarity in fold space.},
      journal = {Bioinformatics},
      year = {2008},
      volume = {24},
      number = {6},
      pages = {872--873},
      url = {http://dx.doi.org/10.1093/bioinformatics/btn040},
      doi = {http://dx.doi.org/10.1093/bioinformatics/btn040}
    }
    					
    Frank, K. & Sippl, M.J. High-performance signal peptide prediction based on sequence alignment techniques. 2008 Bioinformatics
    Vol. 24 (19) , pp. 2172-2176  
    article
    Abstract: The accuracy of current signal peptide predictors is outstanding. The most successful predictors are based on neural networks and hidden Markov models, reaching a sensitivity of 99% and an accuracy of 95 Here, we demonstrate that the popular BLASTP alignment tool can be tuned for signal peptide prediction reaching the same high level of prediction success. Alignment-based techniques provide additional benefits. In spite of high success rates signal peptide predictors yield false predictions. Simple sequences like polyvaline, for example, are predicted as signal peptides. The general architecture of learning systems makes it difficult to trace the cause of such problems. This kind of false predictions can be recognized or avoided altogether by using sequence comparison techniques. Based on these results we have implemented a public web service, called Signal-BLAST. Predictions returned by Signal-BLAST are transparent and easy to analyze. AVAILABILITY: Signal-BLAST is available online at http://sigpep.services.came.sbg.ac.at/signalblast.html.
    BibTeX:
    @article{Frank.Sippl-2008,
      author = {Karl Frank and Manfred J Sippl},
      title = {High-performance signal peptide prediction based on sequence alignment techniques.},
      journal = {Bioinformatics},
      year = {2008},
      volume = {24},
      number = {19},
      pages = {2172--2176},
      url = {http://dx.doi.org/10.1093/bioinformatics/btn422},
      doi = {http://dx.doi.org/10.1093/bioinformatics/btn422}
    }
    					
    Wiederstein, M. & Sippl, M.J. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. 2007 Nucleic Acids Res.
    Vol. 35 (Web Server issue) , pp. W407-W410  
    article
    Abstract: A major problem in structural biology is the recognition of errors in experimental and theoretical models of protein structures. The ProSA program (Protein Structure Analysis) is an established tool which has a large user base and is frequently employed in the refinement and validation of experimental protein structures and in structure prediction and modeling. The analysis of protein structures is generally a difficult and cumbersome exercise. The new service presented here is a straightforward and easy to use extension of the classic ProSA program which exploits the advantages of interactive web-based applications for the display of scores and energy plots that highlight potential problems spotted in protein structures. In particular, the quality scores of a protein are displayed in the context of all known protein structures and problematic parts of a structure are shown and highlighted in a 3D molecule viewer. The service specifically addresses the needs encountered in the validation of protein structures obtained from X-ray analysis, NMR spectroscopy and theoretical calculations. ProSA-web is accessible at https://prosa.services.came.sbg.ac.at.
    BibTeX:
    @article{Wiederstein.Sippl-2007,
      author = {Markus Wiederstein and Manfred J Sippl},
      title = {ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins.},
      journal = {Nucleic Acids Res.},
      year = {2007},
      volume = {35},
      number = {Web Server issue},
      pages = {W407--W410},
      url = {http://dx.doi.org/10.1093/nar/gkm290},
      doi = {http://dx.doi.org/10.1093/nar/gkm290}
    }
    					
    Weichenberger, C.X. & Sippl, M.J. NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures. 2007 Nucleic Acids Res.
    Vol. 35 (Web Server issue) , pp. W403-W406  
    article
    Abstract: The current Protein Data Bank (PDB) contains about 40 000 protein structures with approximately half a million incorrect atom positions resulting from erroneously assigned asparagine (Asn) and glutamine (Gln) rotamers. These errors affect applications in protein structure analysis, modeling and docking and therefore the detection, correction and prevention of such errors is highly desirable. We present NQ-Flipper, a web service based on mean force potentials to automatically detect and correct erroneous Asn and Gln rotamers. The service accepts protein structure files formatted in PDB style or PDB codes. For an Asn/Gln side-chain amide NQ-Flipper computes the total interaction energy with the surrounding atoms as the sum of pairwise atom-atom interaction energies. The energy difference between the original and the alternative rotamers identifies the correct configuration of the amide group. The web service lists the interaction energies of all Asn/Gln residues found in a PDB file and shows the structure and offending residues in an interactive 3D viewer. The corrected protein structure is available for download in various compression formats. The web service is accessible at http://flipper.services.came.sbg.ac.at.
    BibTeX:
    @article{Weichenberger.Sippl-2007,
      author = {Christian X Weichenberger and Manfred J Sippl},
      title = {NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures.},
      journal = {Nucleic Acids Res.},
      year = {2007},
      volume = {35},
      number = {Web Server issue},
      pages = {W403--W406},
      url = {http://dx.doi.org/10.1093/nar/gkm263},
      doi = {http://dx.doi.org/10.1093/nar/gkm263}
    }
    					
    Suhrer, S.J.; Wiederstein, M. & Sippl, M.J. QSCOP - SCOP quantified by structural relationships. 2007 Bioinformatics
    Vol. 23 (4) , pp. 513-514  
    article
    Abstract: The database SCOP (Structural Classification Of Proteins) has become a major resource in bioinformatics and protein science. A particular strength of SCOP is the flexibility of its rules enabling the preservation of the many details spotted by experts in the classification process. Here we endow classic SCOP Families with quantified structural information and comment on the structural diversity found in the SCOP hierarchy. Availability: Quantified SCOP (QSCOP) is available as a public WEB service. http://services.came.sbg.ac.at.
    BibTeX:
    @article{Suhrer.Wiederstein.ea-2007,
      author = {Stefan J Suhrer and Markus Wiederstein and Manfred J Sippl},
      title = {QSCOP -- SCOP quantified by structural relationships.},
      journal = {Bioinformatics},
      year = {2007},
      volume = {23},
      number = {4},
      pages = {513--514},
      url = {http://dx.doi.org/10.1093/bioinformatics/btl594},
      doi = {http://dx.doi.org/10.1093/bioinformatics/btl594}
    }
    					
    Suhrer, S.J.; Gruber, M. & Sippl, M.J. QSCOP-BLAST-fast retrieval of quantified structural information for protein sequences of unknown structure. 2007 Nucleic Acids Research
    Vol. 35 (Web Server issue) , pp. W411-W415  
    article
    Abstract: QSCOP is a quantitative structural classification of proteins which distinguishes itself from other classifications by two essential properties: (i) QSCOP is concurrent with the Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank and (ii) QSCOP covers the widely used SCOP classification with layers of quantitative structural information. The QSCOP-BLAST web server presented here combines the BLAST sequence search engine with QSCOP to retrieve, for a given query sequence, all structural information currently available. The resulting search engine is reliable in terms of the quality of results obtained, and it is efficient in that results are displayed instantaneously. The hierarchical organization of QSCOP is used to control the redundancy and diversity of the retrieved hits with the benefit that the often cumbersome and difficult interpretation of search results is an intuitive and straightforward exercise. We demonstrate the use of QSCOP-BLAST by example. The server is accessible at http://qscop-blast.services.came.sbg.ac.at/
    BibTeX:
    @article{Suhrer.Gruber.ea-2007,
      author = {Stefan J Suhrer and Markus Gruber and Manfred J Sippl},
      title = {QSCOP-BLAST--fast retrieval of quantified structural information for protein sequences of unknown structure.},
      journal = {Nucleic Acids Research},
      year = {2007},
      volume = {35},
      number = {Web Server issue},
      pages = {W411--W415},
      url = {http://dx.doi.org/10.1093/nar/gkm264},
      doi = {http://dx.doi.org/10.1093/nar/gkm264}
    }
    					
    Weichenberger, C.X. & Sippl, M.J. Self-Consistent Assignment of Asparagine and Glutamine Amide Rotamers in Protein Crystal Structures. 2006 Structure
    Vol. 14 (6) , pp. 967-972  
    article
    Abstract: The current protein structure database contains unfavorable Asn/Gln amide rotamers in the order of 20 Here, we derive a set of self-consistent potential functions to identify and correct unfavorable rotamers. Potentials of mean force for all heavy atoms are compiled from a database of high-resolution protein crystal structures. Starting from erroneous data, a refinement-correction cycle quickly converges to a self-consistent set of potentials. The refinement is entirely driven by the deposited structure data and does not involve any assumptions on molecular interactions or any artificial constraints. The refined potentials obtained in this way identify unfavorable rotamers with high confidence. Since the state of Asn/Gln rotamers is largely determined by hydrogen bond interactions, the features of the respective potentials are of interest in terms of molecular interactions, protein structure refinement, and prediction. The Asn/Gln rotamer assignment is available as a public web service intended to support protein structure refinement and modeling.
    BibTeX:
    @article{Weichenberger.Sippl-2006a,
      author = {Christian X Weichenberger and Manfred J Sippl},
      title = {Self-Consistent Assignment of Asparagine and Glutamine Amide Rotamers in Protein Crystal Structures.},
      journal = {Structure},
      year = {2006},
      volume = {14},
      number = {6},
      pages = {967--972},
      url = {http://dx.doi.org/10.1016/j.str.2006.04.002},
      doi = {http://dx.doi.org/10.1016/j.str.2006.04.002}
    }
    					
    Weichenberger, C.X. & Sippl, M.J. NQ-Flipper: validation and correction of asparagine/glutamine amide rotamers in protein crystal structures. 2006 Bioinformatics
    Vol. 22 (11) , pp. 1397-1398  
    article
    Abstract: SUMMARY: The error rate of asparagine (Asn) and glutamine (Gln) amide rotamers in protein crystal structures is in the order of 20% and as a consequence the current Protein Database (PDB) contains approximately half a million incorrect Asn and Gln side-chain rotamers. Here we present NQ-Flipper, a web service based on knowledge-based potentials of mean force to automatically detect and correct erroneous rotamers. We achieve excellent agreement with expert curated data. AVAILABILITY: The program is accessible freely as a web service at http://flipper.services.came.sbg.ac.at CONTACT: sippl@came.sbg.ac.at.
    BibTeX:
    @article{Weichenberger.Sippl-2006,
      author = {Christian X Weichenberger and Manfred J Sippl},
      title = {NQ-Flipper: validation and correction of asparagine/glutamine amide rotamers in protein crystal structures.},
      journal = {Bioinformatics},
      year = {2006},
      volume = {22},
      number = {11},
      pages = {1397--1398},
      url = {http://dx.doi.org/10.1093/bioinformatics/btl128},
      doi = {http://dx.doi.org/10.1093/bioinformatics/btl128}
    }
    					
    Sippl, M. Zbilut, J.P. & Scheibel, T. (Hrsg.) 5 ( Protein structure prediction and molecular forces ) 2006 Protein structure prediction and molecular forces Protein Folding-Misfolding: Some Current Concepts of Protein Chemistry , pp. 117-140   incollection
    BibTeX:
    @incollection{Sippl-2006,
      author = {Manfred Sippl},
      title = {Protein structure prediction and molecular forces},
      booktitle = {Protein Folding-Misfolding: Some Current Concepts of Protein Chemistry},
      publisher = {Nova publishers},
      year = {2006},
      pages = {117-140}
    }
    					
    Wiederstein, M. & Sippl, M.J. Protein sequence randomization: efficient estimation of protein stability using knowledge-based potentials. 2005 J. Mol. Biol.
    Vol. 345 (5) , pp. 1199-1212  
    article
    Abstract: Modifications of the amino acid sequence generally affect protein stability. Here, we use knowledge-based potentials to estimate the stability of protein structures under sequence variation. Calculations on a variety of protein scaffolds result in a clear distinction of known mutable regions from arbitrarily chosen control patches. For example, randomly changing the sequence of an antibody paratope yields a significantly lower number of destabilized mutants as compared to the randomization of comparable regions on the protein surface. The technique is computationally efficient and can be used to screen protein structures for regions that are amenable to molecular tinkering by preserving the stability of the mutated proteins.
    BibTeX:
    @article{Wiederstein.Sippl-2005,
      author = {Wiederstein, M. and Sippl, M. J.},
      title = {Protein sequence randomization: efficient estimation of protein stability using knowledge-based potentials.},
      journal = {J. Mol. Biol.},
      year = {2005},
      volume = {345},
      number = {5},
      pages = {1199--1212},
      url = {http://dx.doi.org/10.1016/j.jmb.2004.11.012},
      doi = {http://dx.doi.org/10.1016/j.jmb.2004.11.012}
    }
    					
    Wiederstein, M.; Lackner, P.; Kienberger, F. & Sippl, M.J. Directed in silico mutagenesis 2004 Evolutionary Methods in Biotechnology (Brakmann,S., Schwienhorst,A. (eds)).
    Vol. 0: , pp. 154-175  
    article
    BibTeX:
    @article{Wiederstein.Lackner.ea-2004,
      author = {Wiederstein, M. and Lackner, P. and Kienberger, F. and Sippl, M. J.},
      title = {Directed in silico mutagenesis},
      journal = {Evolutionary Methods in Biotechnology (Brakmann,S., Schwienhorst,A. (eds)).},
      year = {2004},
      volume = {0:},
      pages = {154--175}
    }
    					
    Prlic, A.; Domingues, F.S.; Lackner, P. & Sippl, M.J. WILMA - automated annotation of protein sequences 2004 Bioinformatics
    Vol. 20 , pp. 127-128  
    article
    BibTeX:
    @article{Prlic.Domingues.ea-2004,
      author = {Prlic, A. and Domingues, F. S. and Lackner, P. and Sippl, M. J.},
      title = {WILMA - automated annotation of protein sequences},
      journal = {Bioinformatics},
      year = {2004},
      volume = {20},
      pages = {127--128}
    }
    					
    Lackner, P.; Muellegger, J.; Reitinger, S. & Lepperdinger, G. Tailor-made recombinant proteins: from computational analysis to practical application 2002 Recent Research Developments in Proteins   incollection
    BibTeX:
    @incollection{Lackner.Muellegger.ea-2002,
      author = {Lackner,P and Muellegger,J and Reitinger,S and Lepperdinger,G},
      title = {Tailor-made recombinant proteins: from computational analysis to practical application},
      booktitle = {Recent Research Developments in Proteins},
      publisher = {Transworld Research Network},
      year = {2002}
    }
    					
    Amberger, A.; Schneeberger, S.; Hernegger, G.; Brandacher, G.; Obrist, P.; Lackner, P.; Margreiter, R. & Mark, W. Gene expression profiling of prolonged cold ischemia and reperfusion in murine heart transplants. 2002 Transplantation.
    Vol. 74 , pp. 1441-1449  
    article
    BibTeX:
    @article{Amberger.Schneeberger.ea-2002,
      author = {Amberger, A. and Schneeberger, S. and Hernegger, G. and Brandacher, G. and Obrist, P. and Lackner, P. and Margreiter, R. and Mark, W.},
      title = {Gene expression profiling of prolonged cold ischemia and reperfusion in murine heart transplants.},
      journal = {Transplantation.},
      year = {2002},
      volume = {74},
      pages = {1441--1449}
    }
    					
    Sippl, M.J.; Lackner, P.; Domingues, F.S.; Prlic, A.; Malik, R.; Andreeva, A. & Wiederstein, M. Assessment of the CASP4 Fold Recognition Category. 2001 Proteins
    Vol. 45 , pp. 55-67  
    article
    BibTeX:
    @article{Sippl.Lackner.ea-2001,
      author = {Sippl, M. J. and Lackner, P. and Domingues, F. S. and Prlic, A. and Malik, R. and Andreeva, A. and Wiederstein, M.},
      title = {Assessment of the CASP4 Fold Recognition Category.},
      journal = {Proteins},
      year = {2001},
      volume = {45},
      pages = {55--67}
    }
    					
    Benhabiles, N.; Lackner, P.; Domingues, F.S.; Wegenkittl, S.; Prlic, A. & Sippl, M.J. Assessing protein models: An evaluation of the performance of different score types. 2001 Rational Approaches to Drug Design.
    Vol. 0: , pp. 99-104  
    article
    BibTeX:
    @article{Benhabiles.Lackner.ea-2001,
      author = {Benhabiles, N. and Lackner, P. and Domingues, F. S. and Wegenkittl, S. and Prlic, A. and Sippl, M. J.},
      title = {Assessing protein models: An evaluation of the performance of different score types.},
      journal = {Rational Approaches to Drug Design.},
      year = {2001},
      volume = {0:},
      pages = {99--104}
    }
    					
    Prlic, A.; Domingues, F.S. & Sippl, M.J. Structure-derived substitution matrices for alignment of distantly related sequences. 2000 Protein Eng.
    Vol. 13 , pp. 545-550  
    article
    BibTeX:
    @article{Prlic.Domingues.ea-2000,
      author = {Prlic, A. and Domingues, F. S. and Sippl, M. J.},
      title = {Structure-derived substitution matrices for alignment of distantly related sequences.},
      journal = {Protein Eng.},
      year = {2000},
      volume = {13},
      pages = {545--550}
    }
    					
    Lackner, P.; Koppensteiner, W.A.; Sippl, M.J. & Domingues, F.S. ProSup: a refined tool for protein structure alignment 2000 Protein Eng.
    Vol. 13 , pp. 745-752  
    article
    BibTeX:
    @article{Lackner.Koppensteiner.ea-2000,
      author = {Lackner, P. and Koppensteiner, W. A. and Sippl, M. J. and Domingues, F. S.},
      title = {ProSup: a refined tool for protein structure alignment},
      journal = {Protein Eng.},
      year = {2000},
      volume = {13},
      pages = {745--752}
    }
    					
    Koppensteiner, W.A.; Lackner, P.; Wiederstein, M. & Sippl, M.J. Characterization of novel proteins based on known protein structures. 2000 J.Mol.Biol.
    Vol. 296 , pp. 1139-1152  
    article
    BibTeX:
    @article{Koppensteiner.Lackner.ea-2000,
      author = {Koppensteiner, W. A. and Lackner, P. and Wiederstein, M. and Sippl, M. J.},
      title = {Characterization of novel proteins based on known protein structures.},
      journal = {J.Mol.Biol.},
      year = {2000},
      volume = {296},
      pages = {1139--1152}
    }
    					
    Domingues, F.S.; Lackner, P.; Andreeva, A. & Sippl, M.J. Structure-based evaluation of sequence comparison and fold recognition alignment accuracy. 2000 J. Mol. Biol.
    Vol. 297 , pp. 1003-1013  
    article
    BibTeX:
    @article{Domingues.Lackner.ea-2000,
      author = {Domingues, F. S. and Lackner, P. and Andreeva, A. and Sippl, M. J.},
      title = {Structure-based evaluation of sequence comparison and fold recognition alignment accuracy.},
      journal = {J. Mol. Biol.},
      year = {2000},
      volume = {297},
      pages = {1003--1013}
    }
    					
    Domingues, F.S.; Koppensteiner, W.A. & Sippl, M.J. The role of protein structure in genomics. 2000 FEBS Lett.
    Vol. 476 , pp. 98-102  
    article
    BibTeX:
    @article{Domingues.Koppensteiner.ea-2000,
      author = {Domingues, F. S. and Koppensteiner, W. A. and Sippl, M. J.},
      title = {The role of protein structure in genomics.},
      journal = {FEBS Lett.},
      year = {2000},
      volume = {476},
      pages = {98--102}
    }
    					
    Sippl, M.J.; Lackner, P.; Domingues, F.S. & Koppensteiner, W.A. An attempt to analyse progress in fold recognition from CASP1 to CASP3. 1999 Proteins.
    Vol. 37 , pp. 226-230  
    article
    BibTeX:
    @article{Sippl.Lackner.ea-1999,
      author = {Sippl, M. J. and Lackner, P. and Domingues, F. S. and Koppensteiner, W. A.},
      title = {An attempt to analyse progress in fold recognition from CASP1 to CASP3.},
      journal = {Proteins.},
      year = {1999},
      volume = {37},
      pages = {226--230}
    }
    					
    Sippl, M.J. Who solved the protein folding problem? 1999 Structure Fold.Des.
    Vol. 7 , pp. R81-R83  
    article
    BibTeX:
    @article{Sippl-1999,
      author = {Sippl, M. J.},
      title = {Who solved the protein folding problem?},
      journal = {Structure Fold.Des.},
      year = {1999},
      volume = {7},
      pages = {R81--R83}
    }
    					
    Lackner, P.; Koppensteiner, W.A.; Domingues, F.S. & Sippl, M.J. Automated large scale evaluation of protein structure predictions. 1999 Proteins.
    Vol. 37 , pp. 7-14  
    article
    BibTeX:
    @article{Lackner.Koppensteiner.ea-1999,
      author = {Lackner, P. and Koppensteiner, W. A. and Domingues, F. S. and Sippl, M. J.},
      title = {Automated large scale evaluation of protein structure predictions.},
      journal = {Proteins.},
      year = {1999},
      volume = {37},
      pages = {7--14}
    }
    					
    Imberty, A.; Monier, C.; Bettler, E.; Morera, S.; Freemont, P.; Sippl, M.; Flockner, H.; Ruger, W. & Breton, C. Fold recognition study of alpha3-galactosyltransferase and molecular modeling of the nucleotide sugar-binding domain. 1999 Glycobiology.
    Vol. 9 , pp. 713-722  
    article
    BibTeX:
    @article{Imberty.Monier.ea-1999,
      author = {Imberty, A. and Monier, C. and Bettler, E. and Morera, S. and Freemont, P. and Sippl, M. and Flockner, H. and Ruger, W. and Breton, C.},
      title = {Fold recognition study of alpha3-galactosyltransferase and molecular modeling of the nucleotide sugar-binding domain.},
      journal = {Glycobiology.},
      year = {1999},
      volume = {9},
      pages = {713--722}
    }
    					
    Hartl, A.; Kiesslich, J.; Weiss, R.; Bernhaupt, A.; Mostbock, S.; Scheiblhofer, S.; Flockner, H.; Sippl, M.; Ebner, C.; Ferreira, F. & Thalhamer, J. Isoforms of the major allergen of birch pollen induce different immune responses after genetic immunization. 1999 Int.Arch.Allergy Immunol.
    Vol. 120 , pp. 17-29  
    article
    BibTeX:
    @article{Hartl.Kiesslich.ea-1999,
      author = {Hartl, A. and Kiesslich, J. and Weiss, R. and Bernhaupt, A. and Mostbock, S. and Scheiblhofer, S. and Flockner, H. and Sippl, M. and Ebner, C. and Ferreira, F. and Thalhamer, J.},
      title = {Isoforms of the major allergen of birch pollen induce different immune responses after genetic immunization.},
      journal = {Int.Arch.Allergy Immunol.},
      year = {1999},
      volume = {120},
      pages = {17--29}
    }
    					
    Domingues, F.S.; Koppensteiner, W.A.; Jaritz, M.; Prlic, A.; Weichenberger, C.; Wiederstein, M.; Floeckner, H.; Lackner, P. & Sippl, M.J. Sustained performance of knowledge-based potentials in fold recognition. 1999 Proteins
    Vol. 37 , pp. 112-120  
    article
    BibTeX:
    @article{Domingues.Koppensteiner.ea-1999,
      author = {Domingues, F. S. and Koppensteiner, W. A. and Jaritz, M. and Prlic, A. and Weichenberger, C. and Wiederstein, M. and Floeckner, H. and Lackner, P. and Sippl, M. J.},
      title = {Sustained performance of knowledge-based potentials in fold recognition.},
      journal = {Proteins},
      year = {1999},
      volume = {37},
      pages = {112--120}
    }
    					
    Koppensteiner, W.A. & Sippl, M.J. Knowledge-based potentials-back to the roots. 1998 Biochemistry (Mosc).
    Vol. 63 , pp. 247-252  
    article
    BibTeX:
    @article{Koppensteiner.Sippl-1998,
      author = {Koppensteiner, W. A. and Sippl, M. J.},
      title = {Knowledge-based potentials--back to the roots.},
      journal = {Biochemistry (Mosc).},
      year = {1998},
      volume = {63},
      pages = {247--252}
    }
    					
    Grandori, R. Systematic fold recognition analysis of the sequences encoded by the genome of Mycoplasma pneumoniae. 1998 Protein Eng.
    Vol. 11 , pp. 1129-1135  
    article
    BibTeX:
    @article{Grandori-1998,
      author = {Grandori, R.},
      title = {Systematic fold recognition analysis of the sequences encoded by the genome of Mycoplasma pneumoniae.},
      journal = {Protein Eng.},
      year = {1998},
      volume = {11},
      pages = {1129--1135}
    }
    					
    Vajda, S.; Sippl, M. & Novotny, J. Empirical potentials and functions for protein folding and binding. 1997 Curr.Opin.Struct.Biol.
    Vol. 7 , pp. 222-228  
    article
    BibTeX:
    @article{Vajda.Sippl.ea-1997,
      author = {Vajda, S. and Sippl, M. and Novotny, J.},
      title = {Empirical potentials and functions for protein folding and binding.},
      journal = {Curr.Opin.Struct.Biol.},
      year = {1997},
      volume = {7},
      pages = {222--228}
    }
    					
    Novotny, J. & Sippl, M.J. Theory and simulation. Old problems, new paradigms. 1997 Curr.Opin.Struct.Biol.
    Vol. 7 , pp. 179-180  
    article
    BibTeX:
    @article{Novotny.Sippl-1997,
      author = {Novotny, J. and Sippl, M. J.},
      title = {Theory and simulation. Old problems, new paradigms.},
      journal = {Curr.Opin.Struct.Biol.},
      year = {1997},
      volume = {7},
      pages = {179--180}
    }
    					
    Flockner, H.; Domingues, F.S. & Sippl, M.J. Protein folds from pair interactions: a blind test in fold recognition. 1997 Proteins Suppl.
    Vol. Suppl 1: , pp. 129-133  
    article
    BibTeX:
    @article{Flockner.Domingues.ea-1997,
      author = {Flockner, H. and Domingues, F. S. and Sippl, M. J.},
      title = {Protein folds from pair interactions: a blind test in fold recognition.},
      journal = {Proteins Suppl.},
      year = {1997},
      volume = {Suppl 1:},
      pages = {129--133}
    }
    					
    Babajide, A.; Hofacker, I.L.; Sippl, M.J. & Stadler, P.F. Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force. 1997 Fold.Des.
    Vol. 2 , pp. 261-269  
    article
    BibTeX:
    @article{Babajide.Hofacker.ea-1997,
      author = {Babajide, A. and Hofacker, I. L. and Sippl, M. J. and Stadler, P. F.},
      title = {Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force.},
      journal = {Fold.Des.},
      year = {1997},
      volume = {2},
      pages = {261--269}
    }
    					
    Wiedemann, P.; Giehl, K.; Almo, S.C.; Fedorov, A.A.; Girvin, M.; Steinberger, P.; Rudiger, M.; Ortner, M.; Sippl, M.; Dolecek, C.; Kraft, D.; Jockusch, B. & Valenta, R. Molecular and structural analysis of a continuous birch profilin epitope defined by a monoclonal antibody. 1996 J.Biol.Chem.
    Vol. 271 , pp. 29915-29921  
    article
    BibTeX:
    @article{Wiedemann.Giehl.ea-1996,
      author = {Wiedemann, P. and Giehl, K. and Almo, S. C. and Fedorov, A. A. and Girvin, M. and Steinberger, P. and Rudiger, M. and Ortner, M. and Sippl, M. and Dolecek, C. and Kraft, D. and Jockusch, B. and Valenta, R.},
      title = {Molecular and structural analysis of a continuous birch profilin epitope defined by a monoclonal antibody.},
      journal = {J.Biol.Chem.},
      year = {1996},
      volume = {271},
      pages = {29915--29921}
    }
    					
    Sippl, M.J.; Ortner, M.; Jaritz, M.; Lackner, P. & Flockner, H. Helmholtz free energies of atom pair interactions in proteins. 1996 Fold. Des.
    Vol. 1 , pp. 289-298  
    article
    BibTeX:
    @article{Sippl.Ortner.ea-1996,
      author = {Sippl, M. J. and Ortner, M. and Jaritz, M. and Lackner, P. and Flockner, H.},
      title = {Helmholtz free energies of atom pair interactions in proteins.},
      journal = {Fold. Des.},
      year = {1996},
      volume = {1},
      pages = {289--298}
    }
    					
    Sippl, M.J. & Flockner, H. Threading thrills and threats. 1996 Structure.
    Vol. 4 , pp. 15-19  
    article
    BibTeX:
    @article{Sippl.Flockner-1996,
      author = {Sippl, M. J. and Flockner, H.},
      title = {Threading thrills and threats.},
      journal = {Structure.},
      year = {1996},
      volume = {4},
      pages = {15--19}
    }
    					
    Sippl, M.J. Helmholtz free energy of peptide hydrogen bonds in proteins. 1996 J. Mol. Biol.
    Vol. 260 , pp. 644-648  
    article
    BibTeX:
    @article{Sippl-1996,
      author = {Sippl, M. J.},
      title = {Helmholtz free energy of peptide hydrogen bonds in proteins.},
      journal = {J. Mol. Biol.},
      year = {1996},
      volume = {260},
      pages = {644--648}
    }
    					
    Lepperdinger, G.; Strobl, B.; Jilek, A.; Weber, A.; Thalhamer, J.; Flockner, H. & Mollay, C. The lipocalin Xlcpl1 expressed in the neural plate of Xenopus laevis embryos is a secreted retinaldehyde binding protein. 1996 Protein Sci.
    Vol. 5 , pp. 1250-1260  
    article
    BibTeX:
    @article{Lepperdinger.Strobl.ea-1996,
      author = {Lepperdinger, G. and Strobl, B. and Jilek, A. and Weber, A. and Thalhamer, J. and Flockner, H. and Mollay, C.},
      title = {The lipocalin Xlcpl1 expressed in the neural plate of Xenopus laevis embryos is a secreted retinaldehyde binding protein.},
      journal = {Protein Sci.},
      year = {1996},
      volume = {5},
      pages = {1250--1260}
    }
    					
    Feng, Z.K. & Sippl, M.J. Optimum superimposition of protein structures: ambiguities and implications. 1996 Fold. Des.
    Vol. 1 , pp. 123-132  
    article
    BibTeX:
    @article{Feng.Sippl-1996,
      author = {Feng, Z. K. and Sippl, M. J.},
      title = {Optimum superimposition of protein structures: ambiguities and implications.},
      journal = {Fold. Des.},
      year = {1996},
      volume = {1},
      pages = {123--132}
    }
    					
    Sippl, M.J.; Weitckus, S. & Flockner, H. Fold recognition. 1995 Modelling of Biomolecular Structures & Mechanisms;Pullman,A ea(eds).
    Vol. 0: , pp. 107-118  
    article
    BibTeX:
    @article{Sippl.Weitckus.ea-1995,
      author = {Sippl, M. J. and Weitckus, S. and Flockner, H.},
      title = {Fold recognition.},
      journal = {Modelling of Biomolecular Structures & Mechanisms;Pullman,A ea(eds).},
      year = {1995},
      volume = {0:},
      pages = {107--118}
    }
    					
    Sippl, M.J. Knowledge-based potentials for proteins. 1995 Curr. Opin. Struct. Biol.
    Vol. 5 , pp. 229-235  
    article
    BibTeX:
    @article{Sippl-1995,
      author = {Sippl, M. J.},
      title = {Knowledge-based potentials for proteins.},
      journal = {Curr. Opin. Struct. Biol.},
      year = {1995},
      volume = {5},
      pages = {229--235}
    }
    					
    Flockner, H.; Braxenthaler, M.; Lackner, P.; Jaritz, M.; Ortner, M. & Sippl, M.J. Progress in fold recognition. 1995 Proteins
    Vol. 23 , pp. 376-386  
    article
    BibTeX:
    @article{Flockner.Braxenthaler.ea-1995,
      author = {Flockner, H. and Braxenthaler, M. and Lackner, P. and Jaritz, M. and Ortner, M. and Sippl, M. J.},
      title = {Progress in fold recognition.},
      journal = {Proteins},
      year = {1995},
      volume = {23},
      pages = {376--386}
    }
    					
    Braxenthaler, M. & Sippl, M.J. Screening genome sequences for known folds. 1995 In:Protein folds:A distance based approach, Bohr,H.&Brunak,S.(eds).
    Vol. 0: , pp. 80-84  
    article
    BibTeX:
    @article{Braxenthaler.Sippl-1995,
      author = {Braxenthaler, M. and Sippl, M. J.},
      title = {Screening genome sequences for known folds.},
      journal = {In:Protein folds:A distance based approach, Bohr,H.&Brunak,S.(eds).},
      year = {1995},
      volume = {0:},
      pages = {80--84}
    }
    					
    Sippl, M.J.; Weitckus, S. & Flockner, H. In search of protein folds. 1994 The protein folding problem & tertiary structure prediction;Merz,LeGrand(eds).
    Vol. 0: , pp. 353-407  
    article
    BibTeX:
    @article{Sippl.Weitckus.ea-1994,
      author = {Sippl, M. J. and Weitckus, S. and Flockner, H.},
      title = {In search of protein folds.},
      journal = {The protein folding problem & tertiary structure prediction;Merz,LeGrand(eds).},
      year = {1994},
      volume = {0:},
      pages = {353--407}
    }
    					
    Sippl, M.J.; Jaritz, M.; Hendlich, M.; Ortner, M. & Lackner, P. Applications of knowledge based mean fields in the determination of protein structures. 1994 Stat.mechanics, protein struct & protein.substrate interactions;Doniach(ed).
    Vol. 0: , pp. 297-315  
    article
    BibTeX:
    @article{Sippl.Jaritz.ea-1994,
      author = {Sippl, M. J. and Jaritz, M. and Hendlich, M. and Ortner, M. and Lackner, P.},
      title = {Applications of knowledge based mean fields in the determination of protein structures.},
      journal = {Stat.mechanics, protein struct & protein.substrate interactions;Doniach(ed).},
      year = {1994},
      volume = {0:},
      pages = {297--315}
    }
    					
    Sippl, M.J. & Jaritz, M. Predictive power of mean force potentials. 1994 Protein Structure by Distance Analysis;Bohr,H.&Brunak,S(eds).
    Vol. 0: , pp. 113-134  
    article
    BibTeX:
    @article{Sippl.Jaritz-1994,
      author = {Sippl, M. J. and Jaritz, M.},
      title = {Predictive power of mean force potentials.},
      journal = {Protein Structure by Distance Analysis;Bohr,H.&Brunak,S(eds).},
      year = {1994},
      volume = {0:},
      pages = {113--134}
    }
    					
    Sippl, M.J. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. 1993 J.Comput.Aided Mol.Des.
    Vol. 7 , pp. 473-501  
    article
    BibTeX:
    @article{Sippl-1993a,
      author = {Sippl, M. J.},
      title = {Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures.},
      journal = {J.Comput.Aided Mol.Des.},
      year = {1993},
      volume = {7},
      pages = {473--501}
    }
    					
    Sippl, M.J. Recognition of errors in three-dimensional structures of proteins. 1993 Proteins
    Vol. 17 , pp. 355-362  
    article
    BibTeX:
    @article{Sippl-1993,
      author = {Sippl, M. J.},
      title = {Recognition of errors in three-dimensional structures of proteins.},
      journal = {Proteins},
      year = {1993},
      volume = {17},
      pages = {355--362}
    }
    					
    Sippl, M.J. & Weitckus, S. Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. 1992 Proteins
    Vol. 13 , pp. 258-271  
    article
    BibTeX:
    @article{Sippl.Weitckus-1992,
      author = {Sippl, M. J. and Weitckus, S.},
      title = {Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations.},
      journal = {Proteins},
      year = {1992},
      volume = {13},
      pages = {258--271}
    }
    					
    Sippl, M.J.; Hendlich, M. & Lackner, P. Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments: development of strategies and construction of models for myoglobin, lysozyme, and thymosin beta 4. 1992 Protein Sci.
    Vol. 1 , pp. 625-640  
    article
    BibTeX:
    @article{Sippl.Hendlich.ea-1992,
      author = {Sippl, M. J. and Hendlich, M. and Lackner, P.},
      title = {Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments: development of strategies and construction of models for myoglobin, lysozyme, and thymosin beta 4.},
      journal = {Protein Sci.},
      year = {1992},
      volume = {1},
      pages = {625--640}
    }
    					
    Casari, G. & Sippl, M.J. Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds. 1992 J.Mol.Biol.
    Vol. 224 , pp. 725-732  
    article
    BibTeX:
    @article{Casari.Sippl-1992,
      author = {Casari, G. and Sippl, M. J.},
      title = {Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds.},
      journal = {J.Mol.Biol.},
      year = {1992},
      volume = {224},
      pages = {725--732}
    }
    					
    Sippl, M.J. & Stegbuchner, H. Superposition of three-dimensional objects: A fast and numerically stable algorithm for the calculation of the matrix of optimal rotation. 1991 Computers Chem.
    Vol. 15 , pp. 73-78  
    article
    BibTeX:
    @article{Sippl.Stegbuchner-1991,
      author = {Sippl, M. J. and Stegbuchner, H.},
      title = {Superposition of three-dimensional objects: A fast and numerically stable algorithm for the calculation of the matrix of optimal rotation.},
      journal = {Computers Chem.},
      year = {1991},
      volume = {15},
      pages = {73--78}
    }
    					
    Paulweber, B.; Wiebusch, H.; Miesenboeck, G.; Funke, H.; Assmann, G.; Hoelzl, B.; Sippl, M.J.; Friedl, W.; Patsch, J.R. & Sandhofer, F. Molecular basis of lipoprotein lipase deficiency in two Austrian families with type I hyperlipoproteinemia. 1991 Atherosclerosis.
    Vol. 86 , pp. 239-250  
    article
    BibTeX:
    @article{Paulweber.Wiebusch.ea-1991,
      author = {Paulweber, B. and Wiebusch, H. and Miesenboeck, G. and Funke, H. and Assmann, G. and Hoelzl, B. and Sippl, M. J. and Friedl, W. and Patsch, J. R. and Sandhofer, F.},
      title = {Molecular basis of lipoprotein lipase deficiency in two Austrian families with type I hyperlipoproteinemia.},
      journal = {Atherosclerosis.},
      year = {1991},
      volume = {86},
      pages = {239--250}
    }
    					
    Sippl, M.J. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. 1990 J. Mol. Biol.
    Vol. 213 , pp. 859-883  
    article
    BibTeX:
    @article{Sippl-1990,
      author = {Sippl, M. J.},
      title = {Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.},
      journal = {J. Mol. Biol.},
      year = {1990},
      volume = {213},
      pages = {859--883}
    }
    					
    Hendlich, M.; Lackner, P.; Weitckus, S.; Floeckner, H.; Froschauer, R.; Gottsbacher, K.; Casari, G. & Sippl, M.J. Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. 1990 J.Mol.Biol.
    Vol. 216 , pp. 167-180  
    article
    BibTeX:
    @article{Hendlich.Lackner.ea-1990,
      author = {Hendlich, M. and Lackner, P. and Weitckus, S. and Floeckner, H. and Froschauer, R. and Gottsbacher, K. and Casari, G. and Sippl, M. J.},
      title = {Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force.},
      journal = {J.Mol.Biol.},
      year = {1990},
      volume = {216},
      pages = {167--180}
    }
    					
    Kuchler, K.; Gmachl, M.; Sippl, M.J. & Kreil, G. Analysis of the cDNA for phospholipase A2 from honeybee venom glands. The deduced amino acid sequence reveals homology to the corresponding vertebrate enzymes. 1989 Eur.J.Biochem.
    Vol. 184 , pp. 249-254  
    article
    BibTeX:
    @article{Kuchler.Gmachl.ea-1989,
      author = {Kuchler, K. and Gmachl, M. and Sippl, M. J. and Kreil, G.},
      title = {Analysis of the cDNA for phospholipase A2 from honeybee venom glands. The deduced amino acid sequence reveals homology to the corresponding vertebrate enzymes.},
      journal = {Eur.J.Biochem.},
      year = {1989},
      volume = {184},
      pages = {249--254}
    }
    					
    Sippl, M.J. & Scheraga, H.A. Cayley-Menger coordinates. 1986 Proc.Natl.Acad.Sci.USA.
    Vol. 83 , pp. 2283-2287  
    article
    BibTeX:
    @article{Sippl.Scheraga-1986,
      author = {Sippl, M. J. and Scheraga, H. A.},
      title = {Cayley-Menger coordinates.},
      journal = {Proc.Natl.Acad.Sci.USA.},
      year = {1986},
      volume = {83},
      pages = {2283--2287}
    }
    					
    Sippl, M.J. & Scheraga, H.A. Solution of the embedding problem and decomposition of symmetric matrices. 1985 Proc.Natl.Acad.Sci.USA.
    Vol. 82 , pp. 2197-2201  
    article
    BibTeX:
    @article{Sippl.Scheraga-1985,
      author = {Sippl, M. J. and Scheraga, H. A.},
      title = {Solution of the embedding problem and decomposition of symmetric matrices.},
      journal = {Proc.Natl.Acad.Sci.USA.},
      year = {1985},
      volume = {82},
      pages = {2197--2201}
    }
    					
    Sippl, M.J.; Nemethy, G. & Scheraga, H.A. Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H...O=C hydrogen bonds from packing configurations. 1984 J.Phys.Chem.
    Vol. 88: , pp. 6231-6233  
    article
    BibTeX:
    @article{Sippl.Nemethy.ea-1984,
      author = {Sippl, M. J. and Nemethy, G. and Scheraga, H. A.},
      title = {Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H...O=C hydrogen bonds from packing configurations.},
      journal = {J.Phys.Chem.},
      year = {1984},
      volume = {88:},
      pages = {6231--6233}
    }
    					
    Sippl, M.J. On the problem of comparing protein structures. Development and applications of a new method for the assessment of structural similarities of polypeptide conformations. 1982 J. Mol. Biol.
    Vol. 156 , pp. 359-388  
    article
    BibTeX:
    @article{Sippl-1982,
      author = {Sippl, M. J.},
      title = {On the problem of comparing protein structures. Development and applications of a new method for the assessment of structural similarities of polypeptide conformations.},
      journal = {J. Mol. Biol.},
      year = {1982},
      volume = {156},
      pages = {359--388}
    }
    					

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