Literature DB >> 20871105

SimiCon: a web tool for protein-ligand model comparison through calculation of equivalent atomic contacts.

Manuel Rueda1, Vsevolod Katritch, Eugene Raush, Ruben Abagyan.   

Abstract

SUMMARY: SimiCon is a web server designed for an automated identification of equivalent protein-ligand atomic contacts in different conformational models of a complex. The contacts are computed with internal coordinate mechanics (ICM) software with respect to molecular symmetry and the results are shown in the browser as text, tables and interactive 3D graphics. The web server can be executed remotely without a browser to allow users to automate multiple calculations. AVAILABILITY: SimiCon is freely available at http://abagyan.ucsd.edu/SimiCon

Mesh：

Substances：

Year:  2010        PMID： 20871105      PMCID： PMC2981495          DOI： 10.1093/bioinformatics/btq504

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


  11 in total

1.  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

2.  CAPRI: a Critical Assessment of PRedicted Interactions.

Authors:  Joël Janin; Kim Henrick; John Moult; Lynn Ten Eyck; Michael J E Sternberg; Sandor Vajda; Ilya Vakser; Shoshana J Wodak
Journal:  Proteins       Date:  2003-07-01

3.  Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions.

Authors:  Zhan Deng; Claudio Chuaqui; Juswinder Singh
Journal:  J Med Chem       Date:  2004-01-15       Impact factor: 7.446

4.  Assessment of docking poses: interactions-based accuracy classification (IBAC) versus crystal structure deviations.

Authors:  Romano T Kroemer; Anna Vulpetti; Joseph J McDonald; Douglas C Rohrer; Jean-Yves Trosset; Fabrizio Giordanetto; Simona Cotesta; Colin McMartin; Mats Kihlén; Pieter F W Stouten
Journal:  J Chem Inf Comput Sci       Date:  2004 May-Jun

Review 5.  Comparing protein-ligand docking programs is difficult.

Authors:  Jason C Cole; Christopher W Murray; J Willem M Nissink; Richard D Taylor; Robin Taylor
Journal:  Proteins       Date:  2005-08-15

6.  Optimizing fragment and scaffold docking by use of molecular interaction fingerprints.

Authors:  Gilles Marcou; Didier Rognan
Journal:  J Chem Inf Model       Date:  2007 Jan-Feb       Impact factor: 4.956

7.  Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins.

Authors:  R Abagyan; M Totrov
Journal:  J Mol Biol       Date:  1994-01-21       Impact factor: 5.469

8.  A new method for publishing three-dimensional content.

Authors:  Eugene Raush; Max Totrov; Brian D Marsden; Ruben Abagyan
Journal:  PLoS One       Date:  2009-10-20       Impact factor: 3.240

Review 9.  How to do an evaluation: pitfalls and traps.

Authors:  Paul C D Hawkins; Gregory L Warren; A Geoffrey Skillman; Anthony Nicholls
Journal:  J Comput Aided Mol Des       Date:  2008-01-23       Impact factor: 3.686

Review 10.  Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008.

Authors:  Mayako Michino; Enrique Abola; Charles L Brooks; J Scott Dixon; John Moult; Raymond C Stevens
Journal:  Nat Rev Drug Discov       Date:  2009-06       Impact factor: 84.694
View more
  6 in total

1.  Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment.

Authors:  Irina Kufareva; Manuel Rueda; Vsevolod Katritch; Raymond C Stevens; Ruben Abagyan
Journal:  Structure       Date:  2011-08-10       Impact factor: 5.006

2.  Methods of protein structure comparison.

Authors:  Irina Kufareva; Ruben Abagyan
Journal:  Methods Mol Biol       Date:  2012

3.  Withasomniferol C, a new potential SARS-CoV-2 main protease inhibitor from the Withania somnifera plant proposed by in silico approaches.

Authors:  Shivananada Kandagalla; Hrvoje Rimac; Krishnamoorthy Gurushankar; Jurica Novak; Maria Grishina; Vladimir Potemkin
Journal:  PeerJ       Date:  2022-06-02       Impact factor: 3.061

4.  Docking and scoring with ICM: the benchmarking results and strategies for improvement.

Authors:  Marco A C Neves; Maxim Totrov; Ruben Abagyan
Journal:  J Comput Aided Mol Des       Date:  2012-05-09       Impact factor: 3.686

5.  ALiBERO: evolving a team of complementary pocket conformations rather than a single leader.

Authors:  Manuel Rueda; Max Totrov; Ruben Abagyan
Journal:  J Chem Inf Model       Date:  2012-09-17       Impact factor: 4.956

6.  Assessment and challenges of ligand docking into comparative models of G-protein coupled receptors.

Authors:  Elizabeth Dong Nguyen; Christoffer Norn; Thomas M Frimurer; Jens Meiler
Journal:  PLoS One       Date:  2013-07-02       Impact factor: 3.240
  6 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.