Protein-Protein Docking: Past, Present, and Future

被引:15
|
作者
Sunny, Sharon [1 ]
Jayaraj, P. B. [1 ]
机构
[1] Natl Inst Technol, Dept Comp Sci & Engn, Calicut, Kerala, India
来源
PROTEIN JOURNAL | 2022年 / 41卷 / 01期
关键词
Protein-protein docking; Deep learning; Artificial intelligence; Nature-inspired algorithms; Geometric algorithms; Searching and scoring; UNITED-RESIDUE MODEL; MOLECULAR-DYNAMICS; WEB SERVER; SCORING FUNCTION; STRUCTURE PREDICTION; AFFINITY PREDICTION; POLYPEPTIDE-CHAINS; INTERACTION SITES; NEURAL-NETWORK; BENCHMARK;
D O I
10.1007/s10930-021-10031-8
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The biological significance of proteins attracted the scientific community in exploring their characteristics. The studies shed light on the interaction patterns and functions of proteins in a living body. Due to their practical difficulties, reliable experimental techniques pave the way for introducing computational methods in the interaction prediction. Automated methods reduced the difficulties but could not yet replace experimental studies as the field is still evolving. Interaction prediction problem being critical needs highly accurate results, but none of the existing methods could offer reliable performance that can parallel with experimental results yet. This article aims to assess the existing computational docking algorithms, their challenges, and future scope. Blind docking techniques are quite helpful when no information other than the individual structures are available. As more and more complex structures are being added to different databases, information-driven approaches can be a good alternative. Artificial intelligence, ruling over the major fields, is expected to take over this domain very shortly.
引用
收藏
页码:1 / 26
页数:26
相关论文
共 50 条
  • [21] Pushing the Backbone in Protein-Protein Docking
    Kuroda, Daisuke
    Gray, Jeffrey J.
    STRUCTURE, 2016, 24 (10) : 1821 - 1829
  • [22] Progress in protein-protein docking approaches
    Li Chun-Hua
    Ma Xiao-Hui
    Chen Wei-Zu
    Wang Cun-Xin
    PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS, 2006, 33 (07) : 616 - 621
  • [23] Protein-protein docking predictions with RosettaDock
    Gray, JJ
    Baker, D
    BIOPHYSICAL JOURNAL, 2004, 86 (01) : 306A - 306A
  • [24] Protein-Protein Interaction Analysis by Docking
    Fink, Florian
    Ederer, Stephan
    Gronwald, Wolfram
    ALGORITHMS, 2009, 2 (01): : 429 - 436
  • [25] Hydrophobic complementarity in protein-protein docking
    Berchanski, A
    Shapira, B
    Eisenstein, M
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2004, 56 (01) : 130 - 142
  • [26] Interolog interfaces in protein-protein docking
    Alsop, James D.
    Mitchell, Julie C.
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2015, 83 (11) : 1940 - 1946
  • [27] Computer Vision for Protein-protein Docking
    Rudden, Lucas S. P.
    Degiacomi, Matteo T.
    Willcocks, Chris G.
    BIOPHYSICAL JOURNAL, 2020, 118 (03) : 305A - 306A
  • [28] Protein-Protein Docking Dealing With the Unknown
    Moreira, Irina S.
    Fernandes, Pedro A.
    Ramos, Maria J.
    JOURNAL OF COMPUTATIONAL CHEMISTRY, 2010, 31 (02) : 317 - 342
  • [29] Principles of flexible protein-protein docking
    Andrusier, Nelly
    Mashiach, Efrat
    Nussinov, Ruth
    Wolfson, Haim J.
    PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2008, 73 (02) : 271 - 289
  • [30] Protein-protein docking with backbone flexibility
    Wang, Chu
    Bradley, Philip
    Baker, David
    JOURNAL OF MOLECULAR BIOLOGY, 2007, 373 (02) : 503 - 519