DR_bind: a web server for predicting DNA-binding residues from the protein structure based on electrostatics, evolution and geometry

被引:40
作者
Chen, Yao Chi [1 ]
Wright, Jon D. [1 ,2 ]
Lim, Carmay [1 ,3 ]
机构
[1] Acad Sinica, Inst Biomed Sci, Taipei 115, Taiwan
[2] Acad Sinica, Genom Res Ctr, Taipei 115, Taiwan
[3] Natl Tsing Hua Univ, Dept Chem, Hsinchu 300, Taiwan
关键词
SITES; SEQUENCE; INFORMATION; CONSURF; CONSERVATION; MUTATION; REGIONS; SURFACE; MOTIFS; DOMAIN;
D O I
10.1093/nar/gks481
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
DR_bind is a web server that automatically predicts DNA-binding residues, given the respective protein structure based on (i) electrostatics, (ii) evolution and (iii) geometry. In contrast to machine-learning methods, DR_bind does not require a training data set or any parameters. It predicts DNA-binding residues by detecting a cluster of conserved, solvent-accessible residues that are electrostatically stabilized upon mutation to Asp(-)/Glu(-). The server requires as input the DNA-binding protein structure in PDB format and outputs a downloadable text file of the predicted DNA-binding residues, a 3D visualization of the predicted residues highlighted in the given protein structure, and a downloadable PyMol script for visualization of the results. Calibration on 83 and 55 non-redundant DNA-bound and DNA-free protein structures yielded a DNA-binding residue prediction accuracy/precision of 90/47% and 88/42%, respectively. Since DR_bind does not require any training using protein-DNA complex structures, it may predict DNA-binding residues in novel structures of DNA-binding proteins resulting from structural genomics projects with no conservation data. The DR_bind server is freely available with no login requirement at http://dnasite.limlab.ibms.sinica.edu.tw.
引用
收藏
页码:W249 / W256
页数:8
相关论文
共 44 条
  • [1] PSSM-based prediction of DNA binding sites in proteins
    Ahmad, S
    Sarai, A
    [J]. BMC BIOINFORMATICS, 2005, 6 (1)
  • [2] Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information
    Ahmad, S
    Gromiha, MM
    Sarai, A
    [J]. BIOINFORMATICS, 2004, 20 (04) : 477 - 486
  • [3] ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
    Ashkenazy, Haim
    Erez, Elana
    Martz, Eric
    Pupko, Tal
    Ben-Tal, Nir
    [J]. NUCLEIC ACIDS RESEARCH, 2010, 38 : W529 - W533
  • [4] The Protein Data Bank
    Berman, HM
    Battistuz, T
    Bhat, TN
    Bluhm, WF
    Bourne, PE
    Burkhardt, K
    Iype, L
    Jain, S
    Fagan, P
    Marvin, J
    Padilla, D
    Ravichandran, V
    Schneider, B
    Thanki, N
    Weissig, H
    Westbrook, JD
    Zardecki, C
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2002, 58 : 899 - 907
  • [5] A graph-theory algorithm for rapid protein side-chain prediction
    Canutescu, AA
    Shelenkov, AA
    Dunbrack, RL
    [J]. PROTEIN SCIENCE, 2003, 12 (09) : 2001 - 2014
  • [6] NAPS: a residue-level nucleic acid-binding prediction server
    Carson, Matthew B.
    Langlois, Robert
    Lu, Hui
    [J]. NUCLEIC ACIDS RESEARCH, 2010, 38 : W431 - W435
  • [7] The Amber biomolecular simulation programs
    Case, DA
    Cheatham, TE
    Darden, T
    Gohlke, H
    Luo, R
    Merz, KM
    Onufriev, A
    Simmerling, C
    Wang, B
    Woods, RJ
    [J]. JOURNAL OF COMPUTATIONAL CHEMISTRY, 2005, 26 (16) : 1668 - 1688
  • [8] Predicting DNA-binding amino acid residues from electrostatic stabilization upon mutation to Asp/Glu and evolutionary conservation
    Chen, Yao Chi
    Wu, Chih Yuan
    Lim, Carmay
    [J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2007, 67 (03) : 671 - 680
  • [9] Common physical basis of macromolecule-binding sites in proteins
    Chen, Yao Chi
    Lim, Carmay
    [J]. NUCLEIC ACIDS RESEARCH, 2008, 36 (22) : 7078 - 7087
  • [10] Predicting RNA-binding sites from the protein structure based on electrostatics, evolution and geometry
    Chen, Yao Chi
    Lim, Carmay
    [J]. NUCLEIC ACIDS RESEARCH, 2008, 36 (05)