Literature DB >> 34499117

INTERCAAT: identifying interface residues between macromolecules.

Steven Grudman1, J Eduardo Fajardo1, Andras Fiser1.   

Abstract

SUMMARY: The Interface Contact definition with Adaptable Atom Types (INTERCAAT) was developed to determine the atomic interactions between molecules that form a known three dimensional structure. First, INTERCAAT creates a Voronoi tessellation where each atom acts as a seed. Interactions are defined by atoms that share a hyperplane and whose distance is less than the sum of each atoms' Van der Waals radii plus the diameter of a solvent molecule. Interacting atoms are then classified and interactions are filtered based on compatibility. INTERCAAT implements an adaptive atom classification method; therefore, it can explore interfaces between a variety macromolecules. AVAILABILITY: Source code is freely available at (https://gitlab.com/fiserlab.org/intercaat). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
© The Author(s) (2021). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Entities:  

Year:  2021        PMID: 34499117      PMCID: PMC8722752          DOI: 10.1093/bioinformatics/btab596

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.931


  8 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

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Authors:  V Sobolev; A Sorokine; J Prilusky; E E Abola; M Edelman
Journal:  Bioinformatics       Date:  1999-04       Impact factor: 6.937

Review 3.  Voronoi and Voronoi-related tessellations in studies of protein structure and interaction.

Authors:  Anne Poupon
Journal:  Curr Opin Struct Biol       Date:  2004-04       Impact factor: 6.809

4.  The choice of sequence homologs included in multiple sequence alignments has a dramatic impact on evolutionary conservation analysis.

Authors:  Nelson Gil; Andras Fiser
Journal:  Bioinformatics       Date:  2019-01-01       Impact factor: 6.937

5.  The interpretation of protein structures: total volume, group volume distributions and packing density.

Authors:  F M Richards
Journal:  J Mol Biol       Date:  1974-01-05       Impact factor: 5.469

6.  Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.

Authors:  Thom Vreven; Iain H Moal; Anna Vangone; Brian G Pierce; Panagiotis L Kastritis; Mieczyslaw Torchala; Raphael Chaleil; Brian Jiménez-García; Paul A Bates; Juan Fernandez-Recio; Alexandre M J J Bonvin; Zhiping Weng
Journal:  J Mol Biol       Date:  2015-07-29       Impact factor: 5.469

7.  NOXclass: prediction of protein-protein interaction types.

Authors:  Hongbo Zhu; Francisco S Domingues; Ingolf Sommer; Thomas Lengauer
Journal:  BMC Bioinformatics       Date:  2006-01-19       Impact factor: 3.169

8.  BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions.

Authors:  Jianyi Yang; Ambrish Roy; Yang Zhang
Journal:  Nucleic Acids Res       Date:  2012-10-18       Impact factor: 16.971

  8 in total

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