Literature DB >> 33950383

Computational Methods for the Elucidation of Protein Structure and Interactions.

Nicholas S Edmunds1, Liam J McGuffin2.   

Abstract

Biologists are increasingly aware of the importance of protein structure in revealing function. The computational tools now exist which allow researchers to model unknown proteins simply on the basis of their primary sequence. However, for the non-specialist bioinformatician, there is a dazzling array of terminology, acronyms, and competing computer software available for this process. This review is intended to highlight the key stages of computational protein structure prediction, as well as explain the reasons behind some of the procedures and list some established workarounds for common pitfalls. Thereafter follows a review of five one-stop servers for start-to-finish structure prediction.

Keywords:  Alignment; Docking; Homology modeling; Quality assessment; Quaternary structure; Refinement; Sequence; Template-based; Template-free; Tertiary structure

Year:  2021        PMID: 33950383     DOI: 10.1007/978-1-0716-1406-8_2

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  63 in total

1.  Protein secondary structure prediction based on position-specific scoring matrices.

Authors:  D T Jones
Journal:  J Mol Biol       Date:  1999-09-17       Impact factor: 5.469

2.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

3.  Inference of macromolecular assemblies from crystalline state.

Authors:  Evgeny Krissinel; Kim Henrick
Journal:  J Mol Biol       Date:  2007-05-13       Impact factor: 5.469

4.  Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

Authors:  W Kabsch; C Sander
Journal:  Biopolymers       Date:  1983-12       Impact factor: 2.505

5.  Large-scale model quality assessment for improving protein tertiary structure prediction.

Authors:  Renzhi Cao; Debswapna Bhattacharya; Badri Adhikari; Jilong Li; Jianlin Cheng
Journal:  Bioinformatics       Date:  2015-06-15       Impact factor: 6.937

6.  JPred4: a protein secondary structure prediction server.

Authors:  Alexey Drozdetskiy; Christian Cole; James Procter; Geoffrey J Barton
Journal:  Nucleic Acids Res       Date:  2015-04-16       Impact factor: 16.971

7.  SCOP2 prototype: a new approach to protein structure mining.

Authors:  Antonina Andreeva; Dave Howorth; Cyrus Chothia; Eugene Kulesha; Alexey G Murzin
Journal:  Nucleic Acids Res       Date:  2013-11-29       Impact factor: 16.971

8.  SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.

Authors:  Marco Biasini; Stefan Bienert; Andrew Waterhouse; Konstantin Arnold; Gabriel Studer; Tobias Schmidt; Florian Kiefer; Tiziano Gallo Cassarino; Martino Bertoni; Lorenza Bordoli; Torsten Schwede
Journal:  Nucleic Acids Res       Date:  2014-04-29       Impact factor: 16.971

9.  CATH: an expanded resource to predict protein function through structure and sequence.

Authors:  Natalie L Dawson; Tony E Lewis; Sayoni Das; Jonathan G Lees; David Lee; Paul Ashford; Christine A Orengo; Ian Sillitoe
Journal:  Nucleic Acids Res       Date:  2016-11-28       Impact factor: 16.971

10.  IntFOLD: an integrated web resource for high performance protein structure and function prediction.

Authors:  Liam J McGuffin; Recep Adiyaman; Ali H A Maghrabi; Ahmad N Shuid; Danielle A Brackenridge; John O Nealon; Limcy S Philomina
Journal:  Nucleic Acids Res       Date:  2019-07-02       Impact factor: 16.971

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