Physical Chemistry Chemical Physics, volume 18, issue 18, pages 12964-12975

Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power

Zhe Wang ¹

Huiyong Sun ¹

Xinsheng Yao ²

Dan Li ¹

Lei Xu ³

Yongdan Li ⁴

Sheng Tian ⁴

Tingjun Hou ^{1, 5}

Show full list: 8 authors

Hide authors affiliations Show authors affiliations: 5 affiliations

College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China |

State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau (SAR), China |

Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China |

⁴

Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China |

⁵

State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China |

Publication type: Journal Article

Publication date: 2016-04-07

Royal Society of Chemistry (RSC)

Journal: Physical Chemistry Chemical Physics

scimago Q2

SJR: 0.721

CiteScore: 5.5

Impact factor: 2.9

ISSN: 14639076, 14639084

DOI: 10.1039/C6CP01555G

Copy DOI

Physical and Theoretical Chemistry

General Physics and Astronomy

Abstract

We evaluated the capabilities of ten molecular docking programs to predict the ligand binding poses (sampling power) and rank the binding affinities (scoring power).

Found

Top-30

Journals

	10 20 30 40 50 60
Journal of Chemical Information and Modeling	Journal of Chemical Information and Modeling, 53, 7.3% Journal of Chemical Information and Modeling 53 publications, 7.3%
International Journal of Molecular Sciences	International Journal of Molecular Sciences, 25, 3.44% International Journal of Molecular Sciences 25 publications, 3.44%
Molecules	Molecules, 23, 3.17% Molecules 23 publications, 3.17%
Journal of Biomolecular Structure and Dynamics	Journal of Biomolecular Structure and Dynamics, 21, 2.89% Journal of Biomolecular Structure and Dynamics 21 publications, 2.89%
Briefings in Bioinformatics	Briefings in Bioinformatics, 17, 2.34% Briefings in Bioinformatics 17 publications, 2.34%
Scientific Reports	Scientific Reports, 15, 2.07% Scientific Reports 15 publications, 2.07%
Journal of Agricultural and Food Chemistry	Journal of Agricultural and Food Chemistry, 14, 1.93% Journal of Agricultural and Food Chemistry 14 publications, 1.93%
Physical Chemistry Chemical Physics	Physical Chemistry Chemical Physics, 13, 1.79% Physical Chemistry Chemical Physics 13 publications, 1.79%
Methods in Molecular Biology	Methods in Molecular Biology, 11, 1.52% Methods in Molecular Biology 11 publications, 1.52%
Frontiers in Pharmacology	Frontiers in Pharmacology, 9, 1.24% Frontiers in Pharmacology 9 publications, 1.24%
Journal of Computer-Aided Molecular Design	Journal of Computer-Aided Molecular Design, 9, 1.24% Journal of Computer-Aided Molecular Design 9 publications, 1.24%
European Journal of Medicinal Chemistry	European Journal of Medicinal Chemistry, 9, 1.24% European Journal of Medicinal Chemistry 9 publications, 1.24%
ACS Omega	ACS Omega, 8, 1.1% ACS Omega 8 publications, 1.1%
Journal of Cheminformatics	Journal of Cheminformatics, 8, 1.1% Journal of Cheminformatics 8 publications, 1.1%
Heliyon	Heliyon, 7, 0.96% Heliyon 7 publications, 0.96%
Journal of Molecular Graphics and Modelling	Journal of Molecular Graphics and Modelling, 7, 0.96% Journal of Molecular Graphics and Modelling 7 publications, 0.96%
Bioorganic Chemistry	Bioorganic Chemistry, 7, 0.96% Bioorganic Chemistry 7 publications, 0.96%
Journal of Medicinal Chemistry	Journal of Medicinal Chemistry, 7, 0.96% Journal of Medicinal Chemistry 7 publications, 0.96%
Frontiers in Chemistry	Frontiers in Chemistry, 6, 0.83% Frontiers in Chemistry 6 publications, 0.83%
Informatics in Medicine Unlocked	Informatics in Medicine Unlocked, 6, 0.83% Informatics in Medicine Unlocked 6 publications, 0.83%
PLoS ONE	PLoS ONE, 6, 0.83% PLoS ONE 6 publications, 0.83%
ACS Chemical Neuroscience	ACS Chemical Neuroscience, 6, 0.83% ACS Chemical Neuroscience 6 publications, 0.83%
Journal of Chemical Theory and Computation	Journal of Chemical Theory and Computation, 6, 0.83% Journal of Chemical Theory and Computation 6 publications, 0.83%
RSC Advances	RSC Advances, 5, 0.69% RSC Advances 5 publications, 0.69%
Pharmaceuticals	Pharmaceuticals, 5, 0.69% Pharmaceuticals 5 publications, 0.69%
Molecular Diversity	Molecular Diversity, 5, 0.69% Molecular Diversity 5 publications, 0.69%
Computational Biology and Chemistry	Computational Biology and Chemistry, 5, 0.69% Computational Biology and Chemistry 5 publications, 0.69%
Journal of Hazardous Materials	Journal of Hazardous Materials, 5, 0.69% Journal of Hazardous Materials 5 publications, 0.69%
Journal of Molecular Structure	Journal of Molecular Structure, 5, 0.69% Journal of Molecular Structure 5 publications, 0.69%
	10 20 30 40 50 60

Publishers

	20 40 60 80 100 120 140 160 180
Elsevier	Elsevier, 162, 22.31% Elsevier 162 publications, 22.31%
American Chemical Society (ACS)	American Chemical Society (ACS), 120, 16.53% American Chemical Society (ACS) 120 publications, 16.53%
Springer Nature	Springer Nature, 103, 14.19% Springer Nature 103 publications, 14.19%
MDPI	MDPI, 69, 9.5% MDPI 69 publications, 9.5%
Wiley	Wiley, 55, 7.58% Wiley 55 publications, 7.58%
Royal Society of Chemistry (RSC)	Royal Society of Chemistry (RSC), 38, 5.23% Royal Society of Chemistry (RSC) 38 publications, 5.23%
Taylor & Francis	Taylor & Francis, 34, 4.68% Taylor & Francis 34 publications, 4.68%
Frontiers Media S.A.	Frontiers Media S.A., 24, 3.31% Frontiers Media S.A. 24 publications, 3.31%
Oxford University Press	Oxford University Press, 21, 2.89% Oxford University Press 21 publications, 2.89%
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 17, 2.34% Cold Spring Harbor Laboratory 17 publications, 2.34%
Bentham Science Publishers Ltd.	Bentham Science Publishers Ltd., 12, 1.65% Bentham Science Publishers Ltd. 12 publications, 1.65%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 8, 1.1% Public Library of Science (PLoS) 8 publications, 1.1%
Institute of Electrical and Electronics Engineers (IEEE)	Institute of Electrical and Electronics Engineers (IEEE), 7, 0.96% Institute of Electrical and Electronics Engineers (IEEE) 7 publications, 0.96%
American Society for Microbiology	American Society for Microbiology, 5, 0.69% American Society for Microbiology 5 publications, 0.69%
Hindawi Limited	Hindawi Limited, 4, 0.55% Hindawi Limited 4 publications, 0.55%
Impact Journals	Impact Journals, 3, 0.41% Impact Journals 3 publications, 0.41%
World Scientific	World Scientific, 3, 0.41% World Scientific 3 publications, 0.41%
Pleiades Publishing	Pleiades Publishing, 3, 0.41% Pleiades Publishing 3 publications, 0.41%
SAGE	SAGE, 2, 0.28% SAGE 2 publications, 0.28%
American Society for Pharmacology and Experimental Therapeutics	American Society for Pharmacology and Experimental Therapeutics, 1, 0.14% American Society for Pharmacology and Experimental Therapeutics 1 publication, 0.14%
IOS Press	IOS Press, 1, 0.14% IOS Press 1 publication, 0.14%
International Union of Crystallography (IUCr)	International Union of Crystallography (IUCr), 1, 0.14% International Union of Crystallography (IUCr) 1 publication, 0.14%
PeerJ	PeerJ, 1, 0.14% PeerJ 1 publication, 0.14%
Pharmaceutical Society of Japan	Pharmaceutical Society of Japan, 1, 0.14% Pharmaceutical Society of Japan 1 publication, 0.14%
Ovid Technologies (Wolters Kluwer Health)	Ovid Technologies (Wolters Kluwer Health), 1, 0.14% Ovid Technologies (Wolters Kluwer Health) 1 publication, 0.14%
Korean Society of Industrial Engineering Chemistry	Korean Society of Industrial Engineering Chemistry, 1, 0.14% Korean Society of Industrial Engineering Chemistry 1 publication, 0.14%
Cambridge University Press	Cambridge University Press, 1, 0.14% Cambridge University Press 1 publication, 0.14%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 1, 0.14% American Association for the Advancement of Science (AAAS) 1 publication, 0.14%
American Institute of Mathematical Sciences (AIMS)	American Institute of Mathematical Sciences (AIMS), 1, 0.14% American Institute of Mathematical Sciences (AIMS) 1 publication, 0.14%
	20 40 60 80 100 120 140 160 180

We do not take into account publications without a DOI.
Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
Statistics recalculated weekly.

Are you a researcher?

Create a profile to get free access to personal recommendations for colleagues and new articles.

Metrics

61 Field Citation Ratio

21 Relative Citation Ratio

Cite this

GOST |

Cite this

GOST Copy

Wang Z. et al. Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power // Physical Chemistry Chemical Physics. 2016. Vol. 18. No. 18. pp. 12964-12975.

GOST all authors (up to 50) Copy

Wang Z., Sun H., Yao X., Li D., Xu L., Li Y., Tian S., Hou T. Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power // Physical Chemistry Chemical Physics. 2016. Vol. 18. No. 18. pp. 12964-12975.

RIS |

Cite this

RIS Copy

TY - JOUR

DO - 10.1039/C6CP01555G

UR - https://doi.org/10.1039/C6CP01555G

TI - Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power

T2 - Physical Chemistry Chemical Physics

AU - Wang, Zhe

AU - Sun, Huiyong

AU - Yao, Xinsheng

AU - Li, Dan

AU - Xu, Lei

AU - Li, Yongdan

AU - Tian, Sheng

AU - Hou, Tingjun

PY - 2016

DA - 2016/04/07

PB - Royal Society of Chemistry (RSC)

SP - 12964-12975

IS - 18

VL - 18

SN - 1463-9076

SN - 1463-9084

ER -

BibTex |

Cite this

BibTex (up to 50 authors) Copy

@article{2016_Wang,

author = {Zhe Wang and Huiyong Sun and Xinsheng Yao and Dan Li and Lei Xu and Yongdan Li and Sheng Tian and Tingjun Hou},

title = {Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power},

journal = {Physical Chemistry Chemical Physics},

year = {2016},

volume = {18},

publisher = {Royal Society of Chemistry (RSC)},

month = {apr},

url = {https://doi.org/10.1039/C6CP01555G},

number = {18},

pages = {12964--12975},

doi = {10.1039/C6CP01555G}

}

MLA

Cite this

MLA Copy

Wang, Zhe, et al. “Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power.” Physical Chemistry Chemical Physics, vol. 18, no. 18, Apr. 2016, pp. 12964-12975. https://doi.org/10.1039/C6CP01555G.

Found error?

Message

Support chat

Publisher

Royal Society of Chemistry (RSC)

Journal

Physical Chemistry Chemical Physics

scimago Q2

SJR

0.721

CiteScore

5.5

Impact factor

2.9

ISSN

14639076 (Print)

14639084 (Electronic)

Profiles

Hou, Tingjun J