Literature DB >> 31879831

Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4.

Sergei Kotelnikov1,2,3, Andrey Alekseenko1,2, Cong Liu1,4, Mikhail Ignatov1,2,5, Dzmitry Padhorny1,2, Emiliano Brini1, Mark Lukin6, Evangelos Coutsias1,2, Ken A Dill1,4,7, Dima Kozakov8,9,10.   

Abstract

We describe a new template-based method for docking flexible ligands such as macrocycles to proteins. It combines Monte-Carlo energy minimization on the manifold, a fast manifold search method, with BRIKARD for complex flexible ligand searching, and with the MELD accelerator of Replica-Exchange Molecular Dynamics simulations for atomistic degrees of freedom. Here we test the method in the Drug Design Data Resource blind Grand Challenge competition. This method was among the best performers in the competition, giving sub-angstrom prediction quality for the majority of the targets.

Entities:  

Keywords:  BACE-1; D3R; Macrocycles; Protein–ligand docking; Template-based docking

Mesh：

Substances：

Year:  2019        PMID： 31879831      PMCID： PMC7553231          DOI： 10.1007/s10822-019-00257-1

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN： 0920-654X            Impact factor:   3.686


  33 in total

1.  Efficient minimization of angle-dependent potentials for polypeptides in internal coordinates.

Authors:  William J Wedemeyer; David Baker
Journal:  Proteins       Date:  2003-11-01

2.  Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.

Authors:  Araz Jakalian; David B Jack; Christopher I Bayly
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

3.  Accelerating molecular simulations of proteins using Bayesian inference on weak information.

Authors:  Alberto Perez; Justin L MacCallum; Ken A Dill
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-08       Impact factor: 11.205

4.  AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.

Authors:  Oleg Trott; Arthur J Olson
Journal:  J Comput Chem       Date:  2010-01-30       Impact factor: 3.376

5.  Energy Minimization on Manifolds for Docking Flexible Molecules.

Authors:  Hanieh Mirzaei; Shahrooz Zarbafian; Elizabeth Villar; Scott Mottarella; Dmitri Beglov; Sandor Vajda; Ioannis Ch Paschalidis; Pirooz Vakili; Dima Kozakov
Journal:  J Chem Theory Comput       Date:  2015-03-10       Impact factor: 6.006

6.  Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics.

Authors:  Evangelos A Coutsias; Katrina W Lexa; Michael J Wester; Sara N Pollock; Matthew P Jacobson
Journal:  J Chem Theory Comput       Date:  2016-08-04       Impact factor: 6.006

7.  Performance of multiple docking and refinement methods in the pose prediction D3R prospective Grand Challenge 2016.

Authors:  Xavier Fradera; Andreas Verras; Yuan Hu; Deping Wang; Hongwu Wang; James I Fells; Kira A Armacost; Alejandro Crespo; Brad Sherborne; Huijun Wang; Zhengwei Peng; Ying-Duo Gao
Journal:  J Comput Aided Mol Des       Date:  2017-09-14       Impact factor: 3.686

8.  An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes.

Authors:  Tanja Kortemme; Alexandre V Morozov; David Baker
Journal:  J Mol Biol       Date:  2003-02-28       Impact factor: 5.469

9.  The impact of side-chain packing on protein docking refinement.

Authors:  Mohammad Moghadasi; Hanieh Mirzaei; Artem Mamonov; Pirooz Vakili; Sandor Vajda; Ioannis Ch Paschalidis; Dima Kozakov
Journal:  J Chem Inf Model       Date:  2015-03-24       Impact factor: 4.956

10.  ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.

Authors:  James A Maier; Carmenza Martinez; Koushik Kasavajhala; Lauren Wickstrom; Kevin E Hauser; Carlos Simmerling
Journal:  J Chem Theory Comput       Date:  2015-07-23       Impact factor: 6.006
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  3 in total

Review 1.  Delta Machine Learning to Improve Scoring-Ranking-Screening Performances of Protein-Ligand Scoring Functions.

Authors:  Chao Yang; Yingkai Zhang
Journal:  J Chem Inf Model       Date:  2022-05-17       Impact factor: 6.162

2.  ClusPro LigTBM: Automated Template-based Small Molecule Docking.

Authors:  Andrey Alekseenko; Sergei Kotelnikov; Mikhail Ignatov; Megan Egbert; Yaroslav Kholodov; Sandor Vajda; Dima Kozakov
Journal:  J Mol Biol       Date:  2019-12-19       Impact factor: 5.469

3.  Actionable Cytopathogenic Host Responses of Human Alveolar Type 2 Cells to SARS-CoV-2.

Authors:  Ryan M Hekman; Adam J Hume; Raghuveera Kumar Goel; Kristine M Abo; Jessie Huang; Benjamin C Blum; Rhiannon B Werder; Ellen L Suder; Indranil Paul; Sadhna Phanse; Ahmed Youssef; Konstantinos D Alysandratos; Dzmitry Padhorny; Sandeep Ojha; Alexandra Mora-Martin; Dmitry Kretov; Peter E A Ash; Mamta Verma; Jian Zhao; J J Patten; Carlos Villacorta-Martin; Dante Bolzan; Carlos Perea-Resa; Esther Bullitt; Anne Hinds; Andrew Tilston-Lunel; Xaralabos Varelas; Shaghayegh Farhangmehr; Ulrich Braunschweig; Julian H Kwan; Mark McComb; Avik Basu; Mohsan Saeed; Valentina Perissi; Eric J Burks; Matthew D Layne; John H Connor; Robert Davey; Ji-Xin Cheng; Benjamin L Wolozin; Benjamin J Blencowe; Stefan Wuchty; Shawn M Lyons; Dima Kozakov; Daniel Cifuentes; Michael Blower; Darrell N Kotton; Andrew A Wilson; Elke Mühlberger; Andrew Emili
Journal:  Mol Cell       Date:  2020-11-19       Impact factor: 17.970
  3 in total

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