Interfaces in molecular docking

被引：4
|
作者：
Mitchell, JC [1 ]
Shahbaz, S [1 ]
Ten Eyck, LF [1 ]
机构：
[1] Univ Calif San Diego, San Diego Supercomp Ctr, La Jolla, CA 92093 USA
来源：
MOLECULAR SIMULATION | 2004年 / 30卷 / 2-3期
关键词：
Fast Atomic Density Evaluation; fast Fourier transforms; fasciculin-acetylcholinesterase; Barnase-Barstar; mutagenesis experiments;
D O I：
10.1080/0892702031000152217
中图分类号：
O64 [物理化学（理论化学）、化学物理学];
学科分类号：
070304 ; 081704 ;
摘要：
The Fast Atomic Density Evaluation (FADE) program analyzes shape complementarity using atomic density methods and fast Fourier transforms (FFT). Statistical results for 184 protein-protein and protein-DNA complexes are presented. Almost all of the interfaces studies were found to be complementary, and the average FADE complementarity score highlighted systems known to have strong shape complementarity at the binding interfaces. Also given is a detailed analysis of the interfaces for Fasciculin-Acetylcholinesterase and Barnase-Barstar to show how shape complementarity relates to site mutagenesis experiments. For these two cases, there was good agreement between interface points of highest complementarity and the location of residues known to be important for binding.
引用
收藏
页码：97 / 106
页数：10
相关论文
共 50 条
  • [1] Rational Prediction of PROTAC-Compatible Protein-Protein Interfaces by Molecular Docking
    Pereira, Gilberto P.
    Jimenez-Garcia, Brian
    Pellarin, Riccardo
    Launay, Guillaume
    Wu, Sangwook
    Martin, Juliette
    Souza, Paulo C. T.
    JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2023, 63 (21) : 6823 - 6833
  • [2] Interolog interfaces in protein-protein docking
    Alsop, James D.
    Mitchell, Julie C.
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2015, 83 (11) : 1940 - 1946
  • [3] Protein Docking with Information on Evolutionary Conserved Interfaces
    Hashmi, Irina
    Akbal-Delibas, Bahar
    Haspel, Nurit
    Shehu, Amarda
    2011 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE WORKSHOPS, 2011, : 358 - 365
  • [4] Docking without docking:: ISEARCH-Prediction of interactions using known interfaces
    Guenther, Stefan
    May, Patrick
    Hoppe, Andreas
    Frommel, Cornelius
    Preissner, Robert
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2007, 69 (04) : 839 - 844
  • [5] Molecular Docking Algorithms
    Dias, Raquel
    de Azevedo, Walter Filgueira, Jr.
    CURRENT DRUG TARGETS, 2008, 9 (12) : 1040 - 1047
  • [6] Progress in molecular docking
    Fan, Jiyu
    Fu, Ailing
    Zhang, Le
    QUANTITATIVE BIOLOGY, 2019, 7 (02) : 83 - 89
  • [7] Progress in molecular docking
    Jiyu Fan
    Ailing Fu
    Le Zhang
    Quantitative Biology, 2019, 7 (02) : 83 - 89
  • [8] Scoring docking conformations using predicted protein interfaces
    Esmaielbeiki, Reyhaneh
    Nebel, Jean-Christophe
    BMC BIOINFORMATICS, 2014, 15
  • [9] Blind predictions of protein interfaces by docking calculations in CAPRI
    Lensink, Marc F.
    Wodak, Shoshana J.
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2010, 78 (15) : 3085 - 3095
  • [10] Docking by Structural Similarity at Protein-Protein Interfaces
    Kundrotas, Petras
    Sinha, Rohita
    Vakser, Ilya A.
    BIOPHYSICAL JOURNAL, 2010, 98 (03) : 196A - 196A
12345