Journal ArticleDOI
SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling.
Nicolas Guex,Manuel C. Peitsch +1 more
TLDR
An environment for comparative protein modeling is developed that consists of SWISS‐MODEL, a server for automated comparativeprotein modeling and of the SWiss‐PdbViewer, a sequence to structure workbench that provides a large selection of structure analysis and display tools.Abstract:
Comparative protein modeling is increasingly gaining interest since it is of great assistance during the rational design of mutagenesis experiments. The availability of this method, and the resulting models, has however been restricted by the availability of expensive computer hardware and software. To overcome these limitations, we have developed an environment for comparative protein modeling that consists of SWISS-MODEL, a server for automated comparative protein modeling and of the SWISS-PdbViewer, a sequence to structure workbench. The Swiss-PdbViewer not only acts as a client for SWISS-MODEL, but also provides a large selection of structure analysis and display tools. In addition, we provide the SWISS-MODEL Repository, a database containing more than 3500 automatically generated protein models. By making such tools freely available to the scientific community, we hope to increase the use of protein structures and models in the process of experiment design.read more
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Journal ArticleDOI
The Protein Data Bank
Helen M. Berman,John D. Westbrook,Zukang Feng,Gary L. Gilliland,Talapady N. Bhat,Helge Weissig,Ilya N. Shindyalov,Philip E. Bourne +7 more
TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Journal ArticleDOI
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
TL;DR: The SWISS-MODEL workspace is a web-based integrated service dedicated to protein structure homology modelling that assists and guides the user in building protein homology models at different levels of complexity.
Journal ArticleDOI
SWISS-MODEL: homology modelling of protein structures and complexes.
Andrew Waterhouse,Andrew Waterhouse,Martino Bertoni,Martino Bertoni,Stefan Bienert,Stefan Bienert,Gabriel Studer,Gabriel Studer,Gerardo Tauriello,Gerardo Tauriello,Rafal Gumienny,Rafal Gumienny,Florian T Heer,Florian T Heer,Tjaart A. P. de Beer,Tjaart A. P. de Beer,Christine Rempfer,Christine Rempfer,Lorenza Bordoli,Lorenza Bordoli,Rosalba Lepore,Rosalba Lepore,Torsten Schwede,Torsten Schwede +23 more
TL;DR: An update to the SWISS-MODEL server is presented, which includes the implementation of a new modelling engine, ProMod3, and the introduction a new local model quality estimation method, QMEANDisCo.
Journal ArticleDOI
SWISS-MODEL: an automated protein homology-modeling server
TL;DR: The SWISS-MODEL server is under constant development to improve the successful implementation of expert knowledge into an easy-to-use server.
Journal ArticleDOI
ExPASy: The proteomics server for in-depth protein knowledge and analysis.
Elisabeth Gasteiger,Alexandre Gattiker,Christine Hoogland,Ivan Ivanyi,Ron D. Appel,Amos Marc Bairoch +5 more
TL;DR: The ExPASy (the Expert Protein Analysis System) World Wide Web server, provided as a service to the life science community by a multidisciplinary team at the Swiss Institute of Bioinformatics, provides access to a variety of databases and analytical tools dedicated to proteins and proteomics.
References
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Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
Bernard R. Brooks,Robert E. Bruccoleri,Barry D. Olafson,David J. States,S. Swaminathan,Martin Karplus +5 more
TL;DR: The CHARMM (Chemistry at Harvard Macromolecular Mechanics) as discussed by the authors is a computer program that uses empirical energy functions to model macromolescular systems, and it can read or model build structures, energy minimize them by first- or second-derivative techniques, perform a normal mode or molecular dynamics simulation, and analyze the structural, equilibrium, and dynamic properties determined in these calculations.
Journal ArticleDOI
Improved tools for biological sequence comparison.
TL;DR: Three computer programs for comparisons of protein and DNA sequences can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity.
Journal ArticleDOI
The Protein Data Bank: a computer-based archival file for macromolecular structures.
Frances C. Bernstein,Thomas F. Koetzle,Graheme J. B. Williams,Edgar F. Meyer,Michael D. Brice,John R. Rodgers,O. Kennard,Takehiko Shimanouchi,Mitsuo Tasumi +8 more
TL;DR: The Protein Data Bank is a computer-based archival file for macromolecular structures that stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies.
Journal ArticleDOI
A new force field for molecular mechanical simulation of nucleic acids and proteins
S. J. Weiner,Peter A. Kollman,David A. Case,U. C. Singh,Caterina Ghio,Giuliano Alagona,Salvatore Profeta,Paul K. Weiner +7 more
TL;DR: In this paper, a force field for simulation of nucleic acids and proteins is presented, which is based on the ECEPP, UNECEPP, and EPEN energy refinement software.