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Literature DB >> 18812365

DOCKGROUND protein-protein docking decoy set.

Abstract

UNLABELLED: A protein-protein docking decoy set is built for the Dockground unbound benchmark set. The GRAMM-X docking scan was used to generate 100 non-native and at least one near-native match per complex for 61 complexes. The set is a publicly available resource for the development of scoring functions and knowledge-based potentials for protein docking methodologies. AVAILABILITY: The decoys are freely available for download at http://dockground.bioinformatics.ku.edu/UNBOUND/decoy/decoy.php

Mesh：

Substances：
Ligands
Proteins

Year: 2008 PMID： 18812365 PMCID： PMC2579708 DOI： 10.1093/bioinformatics/btn497

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

15 in total

1. A systematic study of low-resolution recognition in protein--protein complexes.

Authors: I A Vakser; O G Matar; C F Lam
Journal: Proc Natl Acad Sci U S A Date: 1999-07-20 Impact factor: 11.205

2. Development of unified statistical potentials describing protein-protein interactions.

Authors: Hui Lu; Long Lu; Jeffrey Skolnick
Journal: Biophys J Date: 2003-03 Impact factor: 4.033

3. A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications.

Authors: Ozlem Keskin; Chung-Jung Tsai; Haim Wolfson; Ruth Nussinov
Journal: Protein Sci Date: 2004-04 Impact factor: 6.725

4. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.

Authors: E Katchalski-Katzir; I Shariv; M Eisenstein; A A Friesem; C Aflalo; I A Vakser
Journal: Proc Natl Acad Sci U S A Date: 1992-03-15 Impact factor: 11.205

5. PIBASE: a comprehensive database of structurally defined protein interfaces.

Authors: Fred P Davis; Andrej Sali
Journal: Bioinformatics Date: 2005-01-18 Impact factor: 6.937

6. Development and testing of an automated approach to protein docking.

Authors: Andrei Tovchigrechko; Ilya A Vakser
Journal: Proteins Date: 2005-08-01

7. Protein-Protein Docking Benchmark 2.0: an update.

Authors: Julian Mintseris; Kevin Wiehe; Brian Pierce; Robert Anderson; Rong Chen; Joël Janin; Zhiping Weng
Journal: Proteins Date: 2005-08-01

8. From the Mediterranean coast to the shores of Lake Ontario: CAPRI's premiere on the American continent.

Authors: Shoshana J Wodak
Journal: Proteins Date: 2007-12-01

9. Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex.

Authors: I A Vakser
Journal: Proteins Date: 1997

10. Protein docking for low-resolution structures.

Authors: I A Vakser
Journal: Protein Eng Date: 1995-04

30 in total

1. Salt bridges: geometrically specific, designable interactions.

Authors: Jason E Donald; Daniel W Kulp; William F DeGrado
Journal: Proteins Date: 2011-01-05

2. An information-theoretic classification of amino acids for the assessment of interfaces in protein-protein docking.

Authors: Christophe Jardin; Arno G Stefani; Martin Eberhardt; Johannes B Huber; Heinrich Sticht
Journal: J Mol Model Date: 2013-07-05 Impact factor: 1.810

Review 3. Sampling and scoring: a marriage made in heaven.

Authors: Sandor Vajda; David R Hall; Dima Kozakov
Journal: Proteins Date: 2013-08-19

4. Detecting protein conformational changes in interactions via scaling known structures.

Authors: Fei Guo; Shuai Cheng Li; Wenji Ma; Lusheng Wang
Journal: J Comput Biol Date: 2013-10 Impact factor: 1.479

5. Integrating atom-based and residue-based scoring functions for protein-protein docking.

Authors: Thom Vreven; Howook Hwang; Zhiping Weng
Journal: Protein Sci Date: 2011-08-08 Impact factor: 6.725

6. New benchmark metrics for protein-protein docking methods.

Authors: Mu Gao; Jeffrey Skolnick
Journal: Proteins Date: 2011-03-01

7. Application of information theory to feature selection in protein docking.

Authors: Olaf G Othersen; Arno G Stefani; Johannes B Huber; Heinrich Sticht
Journal: J Mol Model Date: 2011-07-12 Impact factor: 1.810

Review 8. Protein-protein docking: from interaction to interactome.

Authors: Ilya A Vakser
Journal: Biophys J Date: 2014-10-21 Impact factor: 4.033

9. Dockground: A comprehensive data resource for modeling of protein complexes.

Authors: Petras J Kundrotas; Ivan Anishchenko; Taras Dauzhenka; Ian Kotthoff; Daniil Mnevets; Matthew M Copeland; Ilya A Vakser
Journal: Protein Sci Date: 2017-10-10 Impact factor: 6.725

10. Protein docking model evaluation by 3D deep convolutional neural networks.

Authors: Xiao Wang; Genki Terashi; Charles W Christoffer; Mengmeng Zhu; Daisuke Kihara
Journal: Bioinformatics Date: 2020-04-01 Impact factor: 6.937