Literature DB >> 32808340

The AutoDock suite at 30.

David S Goodsell1,2, Michel F Sanner1, Arthur J Olson1, Stefano Forli1.   

Abstract

The AutoDock suite provides a comprehensive toolset for computational ligand docking and drug design and development. The suite builds on 30 years of methods development, including empirical free energy force fields, docking engines, methods for site prediction, and interactive tools for visualization and analysis. Specialized tools are available for challenging systems, including covalent inhibitors, peptides, compounds with macrocycles, systems where ordered hydration plays a key role, and systems with substantial receptor flexibility. All methods in the AutoDock suite are freely available for use and reuse, which has engendered the continued growth of a diverse community of primary users and third-party developers.
© 2020 The Protein Society.

Entities:  

Keywords:  AutoDock; active site prediction; computational docking; computer-aided drug design; force field; peptide-docking

Mesh:

Substances:

Year:  2020        PMID: 32808340      PMCID: PMC7737764          DOI: 10.1002/pro.3934

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  61 in total

1.  Discovery of a novel binding trench in HIV integrase.

Authors:  Julie R Schames; Richard H Henchman; Jay S Siegel; Christoph A Sotriffer; Haihong Ni; J Andrew McCammon
Journal:  J Med Chem       Date:  2004-04-08       Impact factor: 7.446

2.  Protein-ligand docking with multiple flexible side chains.

Authors:  Yong Zhao; Michel F Sanner
Journal:  J Comput Aided Mol Des       Date:  2007-11-22       Impact factor: 3.686

3.  Automated docking of substrates to proteins by simulated annealing.

Authors:  D S Goodsell; A J Olson
Journal:  Proteins       Date:  1990

4.  Covalent docking using autodock: Two-point attractor and flexible side chain methods.

Authors:  Giulia Bianco; Stefano Forli; David S Goodsell; Arthur J Olson
Journal:  Protein Sci       Date:  2015-07-07       Impact factor: 6.725

5.  Comprehensive Evaluation of Fourteen Docking Programs on Protein-Peptide Complexes.

Authors:  Gaoqi Weng; Junbo Gao; Zhe Wang; Ercheng Wang; Xueping Hu; Xiaojun Yao; Dongsheng Cao; Tingjun Hou
Journal:  J Chem Theory Comput       Date:  2020-05-06       Impact factor: 6.006

6.  A geometric approach to macromolecule-ligand interactions.

Authors:  I D Kuntz; J M Blaney; S J Oatley; R Langridge; T E Ferrin
Journal:  J Mol Biol       Date:  1982-10-25       Impact factor: 5.469

7.  Repurposing Triphenylmethane Dyes to Bind to Trimers Derived from Aβ.

Authors:  Patrick J Salveson; Sepehr Haerianardakani; Alexander Thuy-Boun; Stan Yoo; Adam G Kreutzer; Borries Demeler; James S Nowick
Journal:  J Am Chem Soc       Date:  2018-09-06       Impact factor: 15.419

8.  The AutoDock suite at 30.

Authors:  David S Goodsell; Michel F Sanner; Arthur J Olson; Stefano Forli
Journal:  Protein Sci       Date:  2020-09-12       Impact factor: 6.725

9.  Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease.

Authors:  Nanjie Deng; Stefano Forli; Peng He; Alex Perryman; Lauren Wickstrom; R S K Vijayan; Theresa Tiefenbrunn; David Stout; Emilio Gallicchio; Arthur J Olson; Ronald M Levy
Journal:  J Phys Chem B       Date:  2014-09-17       Impact factor: 2.991

10.  Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket.

Authors:  Pierrick Craveur; Anna T Gres; Karen A Kirby; Dandan Liu; John A Hammond; Yisong Deng; Stefano Forli; David S Goodsell; James R Williamson; Stefan G Sarafianos; Arthur J Olson
Journal:  mBio       Date:  2019-03-12       Impact factor: 7.867

View more
  14 in total

1.  Accelerating AutoDock Vina with GPUs.

Authors:  Shidi Tang; Ruiqi Chen; Mengru Lin; Qingde Lin; Yanxiang Zhu; Ji Ding; Haifeng Hu; Ming Ling; Jiansheng Wu
Journal:  Molecules       Date:  2022-05-09       Impact factor: 4.927

2.  Identification of DPP4/CTNNB1/MET as a Theranostic Signature of Thyroid Cancer and Evaluation of the Therapeutic Potential of Sitagliptin.

Authors:  Sheng-Yao Cheng; Alexander T H Wu; Gaber El-Saber Batiha; Ching-Liang Ho; Jih-Chin Lee; Halimat Yusuf Lukman; Mohammed Alorabi; Abdullah N AlRasheedi; Jia-Hong Chen
Journal:  Biology (Basel)       Date:  2022-02-17

3.  The AutoDock suite at 30.

Authors:  David S Goodsell; Michel F Sanner; Arthur J Olson; Stefano Forli
Journal:  Protein Sci       Date:  2020-09-12       Impact factor: 6.725

4.  Identification of evolutionarily stable sites across the SARS-CoV-2 proteome.

Authors:  Chen Wang; Daniel M Konecki; David C Marciano; Harikumar Govindarajan; Amanda M Williams; Brigitta Wastuwidyaningtyas; Thomas Bourquard; Panagiotis Katsonis; Olivier Lichtarge
Journal:  Res Sq       Date:  2020-10-20

5.  Hiltonol Cocktail Kills Lung Cancer Cells by Activating Cancer-Suppressors, PKR/OAS, and Restraining the Tumor Microenvironment.

Authors:  Shu-Chun Chang; Bo-Xiang Zhang; Emily Chia-Yu Su; Wei-Ciao Wu; Tsung-Han Hsieh; Andres M Salazar; Yen-Kuang Lin; Jeak Ling Ding
Journal:  Int J Mol Sci       Date:  2021-02-05       Impact factor: 5.923

6.  Biochemical and structural characterization of quizalofop-resistant wheat acetyl-CoA carboxylase.

Authors:  Raven Bough; Franck E Dayan
Journal:  Sci Rep       Date:  2022-01-13       Impact factor: 4.379

7.  NeuralDock: Rapid and Conformation-Agnostic Docking of Small Molecules.

Authors:  Congzhou M Sha; Jian Wang; Nikolay V Dokholyan
Journal:  Front Mol Biosci       Date:  2022-03-22

8.  Identification of ligand binding sites in intrinsically disordered proteins with a differential binding score.

Authors:  Qiao-Hong Chen; V V Krishnan
Journal:  Sci Rep       Date:  2021-11-19       Impact factor: 4.379

9.  Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and greater coronavirus family.

Authors:  Chen Wang; Daniel M Konecki; David C Marciano; Harikumar Govindarajan; Amanda M Williams; Brigitta Wastuwidyaningtyas; Thomas Bourquard; Panagiotis Katsonis; Olivier Lichtarge
Journal:  Bioinformatics       Date:  2021-05-27       Impact factor: 6.931

10.  Insulin Complexation with Cyclodextrins-A Molecular Modeling Approach.

Authors:  Pálma Bucur; Ibolya Fülöp; Emese Sipos
Journal:  Molecules       Date:  2022-01-11       Impact factor: 4.411

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.