Automated docking of substrates to proteins by simulated annealing

David S. Goodsell; Arthur J. Olson

doi:10.1002/prot.340080302

journal article Jan 01, 1990

Automated docking of substrates to proteins by simulated annealing

David S. Goodsell

Arthur J. Olson

Proteins: Structure, Function, and Bioinformatics Vol. 8 No. 3 pp. 195-202 · Wiley

View at Publisher Save 10.1002/prot.340080302

Abstract

AbstractThe Metropolis technique of conformation searching is combined with rapid energy evaluation using molecular affinity potentials to give an efficient procedure for docking substrates to macromolecules of known structure. The procedure works well on a number of crystallographic test systems, functionally reproducing the observed binding modes of several substrates.

Topics

No keywords indexed for this article. Browse by subject →

References

21

[1]

10.1016/0263-7855(87)80031-0

[2]

COMPOUNDS DESIGNED TO FIT A SITE OF KNOWN STRUCTURE IN HUMAN HAEMOGLOBIN

C.R. BEDDELL, P.J. GOODFORD, F.E. NORRINGTON et al.

British Journal of Pharmacology 10.1111/j.1476-5381.1976.tb07468.x

[3]

10.1021/ja00323a048

[4]

Computer graphics in drug design: molecular modeling of thyroid hormone-prealbumin interactions

Jeffrey M. Blaney, Eugene C. Jorgensen, Michael L. Connolly et al.

Journal of Medicinal Chemistry 10.1021/jm00349a004

[5]

Computer analysis of protein-protein interaction

Shoshana J. Wodak, Joël Janin

Journal of Molecular Biology 10.1016/0022-2836(78)90302-9

[6]

10.1016/0263-7855(84)80033-8

[7]

10.1021/jm00155a023

[8]

A geometric approach to macromolecule-ligand interactions

Irwin D. Kuntz, Jeffrey M. Blaney, Stuart J. Oatley et al.

Journal of Molecular Biology 10.1016/0022-2836(82)90153-x

[9]

10.1002/bip.360260602

[10]

Equation of State Calculations by Fast Computing Machines

Nicholas Metropolis, Arianna W. Rosenbluth, Marshall N. Rosenbluth et al.

The Journal of Chemical Physics 10.1063/1.1699114

[11]

Optimization by Simulated Annealing

S. Kirkpatrick, C. D. Gelatt, M. P. Vecchi

Science 10.1126/science.220.4598.671

[12]

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

P. J. Goodford

Journal of Medicinal Chemistry 10.1021/jm00145a002

[13]

10.1007/bf01590996

[14]

10.1073/pnas.71.11.4298

[15]

10.1016/0022-2836(69)90426-4

[16]

Imoto T. (1972)

[17]

10.1073/pnas.86.10.3639

[18]

10.1021/bk-1988-0372.ch017

[19]

A new force field for molecular mechanical simulation of nucleic acids and proteins

Scott J. Weiner, Peter A. Kollman, David A. Case et al.

Journal of the American Chemical Society 10.1021/ja00315a051

[20]

Rendering volumetric data in molecular systems

David S. Goodsell, I.Saira Mian, Arthur J. Olson

Journal of Molecular Graphics 10.1016/0263-7855(89)80055-4

[21]

10.1016/0097-8485(85)80011-5

Cited By

1,093

Rubiginoids A–N, phytocannabinoid-like meroterpenoids with diverse ring systems from Rhododendron rubiginosum

Mu-Yuan Yu, E-E Luo · 2026

Bioorganic Chemistry

Chemoenzymatic Diazo Synthesis Enabled by Enzymatic Halide Recycling with Vanadium-Dependent Haloperoxidases

Manik Sharma, Yue Li · 2026

Journal of the American Chemical So...

Structure-Based Design of Novel MAO-B Inhibitors: A Review

Emilio Mateev, Maya Georgieva · 2023

Molecules

Molecular docking in organic, inorganic, and hybrid systems: a tutorial review

Madhuchhanda Mohanty, Priti S. Mohanty · 2023

Monatshefte f�r Chemie

DOCK 6: Incorporating hierarchical traversal through precomputed ligand conformations to enable large‐scale docking

Trent E. Balius, Y. Stanley Tan · 2023

Journal of Computational Chemistry

Antagonistic interactions between odorants alter human odor perception

Yosuke Fukutani, Masashi Abe · 2023

Current Biology

Pitstop‐2 and its novel derivative RVD ‐127 disrupt global cell dynamics and nuclear pores integrity by direct interaction with small GTPases

Ivan Liashkovich, Sílvio Terra Stefanello · 2022

Bioengineering & Translational...

First Insight into the Formation of In Vivo Transformation Products of 2-Ethylhexyl diphenyl phosphate in Zebrafish and Prediction of Their Potential Toxicities

Rongyan Yang, Yongxiu Ye · 2022

Environmental Science & Technol...

Scoring Functions for Protein-Ligand Binding Affinity Prediction Using Structure-based Deep Learning: A Review

Rocco Meli, Garrett M. Morris · 2022

Frontiers in Bioinformatics

Molecular modeling in drug discovery

Temitope Isaac Adelusi, Abdul-Quddus Kehinde Oyedele · 2022

Informatics in Medicine Unlocked

Accelerating A uto D ock 4 with GPUs and Gradient-Based Local Search

Diogo Santos-Martins, Leonardo Solis-Vasquez · 2021

Journal of Chemical Theory and Comp...

TheAutoDocksuite at 30

David S. Goodsell, Michel F. Sanner · 2020

Protein Science

Design, synthesis and molecular docking studies of quinazolin-4-ones linked to 1,2,3-triazol hybrids as Mycobacterium tuberculosis H37Rv inhibitors besides antimicrobial activity

Narendra Kumar Maddali, I. V. Kasi Viswanath* · 2019

Medicinal Chemistry Research

Molecular Docking: Shifting Paradigms in Drug Discovery

Luca Pinzi, Giulio Rastelli · 2019

International Journal of Molecular...

Design, Synthesis and Molecular Docking Studies of Novel Pyrazole Benzimidazole Derivatives as Potent Antibacterial Agents

Srinivasa Rao Dasari, Subbaiah Tondepu · 2019

Asian Journal of Chemistry

Ultra-large library docking for discovering new chemotypes

Jiankun Lyu, Sheng Wang · 2019

Nature

Toward Expanded Diversity of Host–Guest Interactions via Synthesis and Characterization of Cyclodextrin Derivatives

K. Kellett, S. A. Kantonen · 2018

Journal of Solution Chemistry

Evaluation of AutoDock and AutoDock Vina on the CASF-2013 Benchmark

Thomas Gaillard · 2018

Journal of Chemical Information and...

Software for molecular docking: a review

Nataraj S. Pagadala, Khajamohiddin Syed · 2017

Biophysical Reviews

Efficient conformational sampling and weak scoring in docking programs? Strategy of the wisdom of crowds

Ludovic Chaput, Liliane Mouawad · 2017

Journal of Cheminformatics

Metrics

1,093

Citations

21

References

Details

Published: Jan 01, 1990
Vol/Issue: 8(3)
Pages: 195-202
License: View

Authors

D

David S. Goodsell

Rutgers, The State University of New Jersey

A

Arthur J. Olson

Scripps Research Institute

Cite This Article

David S. Goodsell, Arthur J. Olson (1990). Automated docking of substrates to proteins by simulated annealing. Proteins: Structure, Function, and Bioinformatics, 8(3), 195-202. https://doi.org/10.1002/prot.340080302

Automated docking of substrates to proteins by simulated annealing

You May Also Like