Literature DB >> 22113833

Let's get honest about sampling.

David L Mobley1.   

Abstract

Molecular simulations see widespread and increasing use in computation and molecular design, especially within the area of molecular simulations applied to biomolecular binding and interactions, our focus here. However, force field accuracy remains a concern for many practitioners, and it is often not clear what level of accuracy is really needed for payoffs in a discovery setting. Here, I argue that despite limitations of today's force fields, current simulation tools and force fields now provide the potential for real benefits in a variety of applications. However, these same tools also provide irreproducible results which are often poorly interpreted. Continued progress in the field requires more honesty in assessment and care in evaluation of simulation results, especially with respect to convergence.

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Year:  2011        PMID: 22113833     DOI: 10.1007/s10822-011-9497-y

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


  25 in total

1.  How fast-folding proteins fold.

Authors:  Kresten Lindorff-Larsen; Stefano Piana; Ron O Dror; David E Shaw
Journal:  Science       Date:  2011-10-28       Impact factor: 47.728

2.  Method for computing protein binding affinity.

Authors:  Charles F F Karney; Jason E Ferrara; Stephan Brunner
Journal:  J Comput Chem       Date:  2005-02       Impact factor: 3.376

3.  Alchemical free energy calculations and multiple conformational substates.

Authors:  Martin Leitgeb; Christian Schröder; Stefan Boresch
Journal:  J Chem Phys       Date:  2005-02-22       Impact factor: 3.488

4.  Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics.

Authors:  Guha Jayachandran; Michael R Shirts; Sanghyun Park; Vijay S Pande
Journal:  J Chem Phys       Date:  2006-08-28       Impact factor: 3.488

5.  On the use of orientational restraints and symmetry corrections in alchemical free energy calculations.

Authors:  David L Mobley; John D Chodera; Ken A Dill
Journal:  J Chem Phys       Date:  2006-08-28       Impact factor: 3.488

6.  Predicting absolute ligand binding free energies to a simple model site.

Authors:  David L Mobley; Alan P Graves; John D Chodera; Andrea C McReynolds; Brian K Shoichet; Ken A Dill
Journal:  J Mol Biol       Date:  2007-06-08       Impact factor: 5.469

7.  Massively parallel computation of absolute binding free energy with well-equilibrated states.

Authors:  Hideaki Fujitani; Yoshiaki Tanida; Azuma Matsuura
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-02-26

8.  Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-ligand Complexes.

Authors:  John C Faver; Mark L Benson; Xiao He; Benjamin P Roberts; Bing Wang; Michael S Marshall; Matthew R Kennedy; C David Sherrill; Kenneth M Merz
Journal:  J Chem Theory Comput       Date:  2011-03-08       Impact factor: 6.006

9.  The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities.

Authors:  Emilio Gallicchio; Mauro Lapelosa; Ronald M Levy
Journal:  J Chem Theory Comput       Date:  2010-09-14       Impact factor: 6.006

10.  Molecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site.

Authors:  Jozica Dolenc; Chris Oostenbrink; Joze Koller; Wilfred F van Gunsteren
Journal:  Nucleic Acids Res       Date:  2005-02-01       Impact factor: 16.971

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  35 in total

1.  BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge.

Authors:  Emilio Gallicchio; Haoyuan Chen; He Chen; Michael Fitzgerald; Yang Gao; Peng He; Malathi Kalyanikar; Chuan Kao; Beidi Lu; Yijie Niu; Manasi Pethe; Jie Zhu; Ronald M Levy
Journal:  J Comput Aided Mol Des       Date:  2015-03-01       Impact factor: 3.686

2.  Perspective: Alchemical free energy calculations for drug discovery.

Authors:  David L Mobley; Pavel V Klimovich
Journal:  J Chem Phys       Date:  2012-12-21       Impact factor: 3.488

Review 3.  Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design.

Authors:  John D Chodera; David L Mobley
Journal:  Annu Rev Biophys       Date:  2013       Impact factor: 12.981

4.  Comparing Alchemical Free Energy Estimates to Experimental Values Based on the Ben-Naim Formula: How Much Agreement Can We Expect?

Authors:  T Ryan Rogers; Feng Wang
Journal:  J Phys Chem B       Date:  2020-01-23       Impact factor: 2.991

5.  Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo.

Authors:  Kalistyn H Burley; Samuel C Gill; Nathan M Lim; David L Mobley
Journal:  J Chem Theory Comput       Date:  2019-02-11       Impact factor: 6.006

6.  Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge.

Authors:  Emilio Gallicchio; Nanjie Deng; Peng He; Lauren Wickstrom; Alexander L Perryman; Daniel N Santiago; Stefano Forli; Arthur J Olson; Ronald M Levy
Journal:  J Comput Aided Mol Des       Date:  2014-02-07       Impact factor: 3.686

7.  Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process.

Authors:  Lauren Wickstrom; Peng He; Emilio Gallicchio; Ronald M Levy
Journal:  J Chem Theory Comput       Date:  2013-07-09       Impact factor: 6.006

8.  Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations.

Authors:  Bing Xie; Trung Hai Nguyen; David D L Minh
Journal:  J Chem Theory Comput       Date:  2017-05-01       Impact factor: 6.006

9.  A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.

Authors:  Rajat Kumar Pal; Kamran Haider; Divya Kaur; William Flynn; Junchao Xia; Ronald M Levy; Tetiana Taran; Lauren Wickstrom; Tom Kurtzman; Emilio Gallicchio
Journal:  J Comput Aided Mol Des       Date:  2016-09-30       Impact factor: 3.686

10.  Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics.

Authors:  Kai Wang; John D Chodera; Yanzhi Yang; Michael R Shirts
Journal:  J Comput Aided Mol Des       Date:  2013-12-03       Impact factor: 3.686

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