- Ofran Y, Mysore V, Rost B (2007) Prediction
of DNA-binding residues from sequence. Bio-
informatics 23(13):I347–I353 - Hwang S, Gou ZK, Kuznetsov IB (2007)
DP-Bind: a Web server for sequence-based pre-
diction of DNA-binding residues in
DNA-binding proteins. Bioinformatics 23
(5):634–636 - Ho SY, FC Y, Chang CY, Huang HL (2007)
Design of accurate predictors for
DNA-binding sites in proteins using hybrid
SVM-PSSM method. Biosystems 90
(1):234–241 - Wang LJ, Brown SJ (2006) BindN: a
web-based tool for efficient prediction of
DNA and RNA binding sites in amino acid
sequences. Nucleic Acids Res 34:W243–W248 - Wang L, Brown SJ (2006) Prediction of
DNA-binding residues from sequence features.
J Bioinform Comput Biol 4(6):1141–1158 - Ahmad S, Gromiha MM, Sarai A (2004) Anal-
ysis and prediction of DNA-binding proteins
and their binding residues based on composi-
tion, sequence and structural information. Bio-
informatics 20(4):477–486 - Yan J, Kurgan L (2017) DRNApred, fast
sequence-based method that accurately pre-
dicts and discriminates DNA- and
RNA-binding residues. Nucleic Acids Res 45
(10):e84 - Ahmad S, Sarai A (2005) PSSM-based predic-
tion of DNA binding sites in proteins. BMC
Bioinformatics 6:33 - Zhu X, Ericksen SS, Mitchell JC (2013) DBSI:
DNA-binding site identifier. Nucleic Acids Res
41(16):e160 - Tsuchiya Y, Kinoshita K, Nakamura H (2004)
Structure-based prediction of DNA-binding
sites on proteins using the empirical preference
of electrostatic potential and the shape of
molecular surfaces. Protein Struct Funct Bioin-
formatics 55(4):885–894 - Chen YC, CY W, Lim C (2007) Predicting
DNA-binding amino acid residues from elec-
trostatic stabilization upon mutation to
Asp/Glu and evolutionary conservation. Pro-
teins 67(3):671–680 - Bhardwaj N, Lu H (2007) Residue-level pre-
diction of DNA-binding sites and its applica-
tion on DNA-binding protein predictions.
FEBS Lett 581(5):1058–1066 - Zhou W, Yan H (2010) A discriminatory func-
tion for prediction of protein-DNA interac-
tions based on alpha shape modeling.
Bioinformatics 26(20):2541–2548
41. Zhou P, Tian F, Ren Y, Shang Z (2010) Sys-
tematic classification and analysis of themes in
protein-DNA recognition. J Chem Inf Model
50(8):1476–1488
42. Sonavane S, Chakrabarti P (2009) Cavities in
protein-DNA and protein-RNA interfaces.
Nucleic Acids Res 37(14):4613–4620
43. Xiong Y, Liu J, Wei DQ (2011) An accurate
feature-based method for identifying
DNA-binding residues on protein surfaces.
Proteins 79(2):509–517
44. Tjong H, Zhou HX (2007) DISPLAR: an
accurate method for predicting DNA-binding
sites on protein surfaces. Nucleic Acids Res 35
(5):1465–1477
45. Jones S, Shanahan HP, Berman HM, Thornton
JM (2003) Using electrostatic potentials to
predict DNA-binding sites on DNA-binding
proteins. Nucleic Acids Res 31
(24):7189–7198
46. Dai H, Xu Q, Xiong Y, Liu WL, Wei DQ
(2016) Improved prediction of michaelis con-
stants in CYP450-mediated reactions by resil-
ient back propagation algorithm. Curr Drug
Metab 17(7):673–680
47. Yao Y, Zhang T, Xiong Y, Li L, Huo J, Wei DQ
(2011) Mutation probability of cytochrome
P450 based on a genetic algorithm and support
vector machine. Biotechnol J 6
(11):1367–1376
48. Xiong Y, Liu J, Zhang W, Zeng T (2012) Pre-
diction of heme binding residues from protein
sequences with integrative sequence profiles.
Proteome Sci 10(Suppl 1):S20
49. Li L, Xiong Y, Zhang ZY, Guo Q, Xu Q, Liow
HH, Zhang YH, Wei DQ (2015) Improved
feature-based prediction of SNPs in human
cytochrome P450 enzymes. Interdiscip Sci
Comput Life Sci 7(1):65–77
50. Zhang W, Xiong Y, Zhao M, Zou H, Ye X, Liu
J (2011) Prediction of conformational B-cell
epitopes from 3D structures by random forests
with a distance-based feature. BMC Bioinfor-
matics 12:341
51. Xu Q, Xiong Y, Dai H, Kumari KM, Xu Q,
HY O, Wei DQ (2017) PDC-SGB: prediction
of effective drug combinations using a stochas-
tic gradient boosting algorithm. J Theor Biol
417:1–7
52. Sun Y, Xiong Y, Xu Q, Wei D (2014) A
hadoop-based method to predict potential
effective drug combination. Biomed Res Int
2014:196858
53. Tsuchiya Y, Kinoshita K, Nakamura H (2005)
PreDs: a server for predicting dsDNA-binding
Survey of Computational Approaches for Prediction of DNA-Binding Residues... 233