1
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Fass J, York F, Wittmann M, Kaus J, Zhao Y. Local Resampling Trick for Focused Molecular Dynamics. J Chem Theory Comput 2023; 19:6139-6150. [PMID: 37706456 DOI: 10.1021/acs.jctc.3c00539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can lead to incorrect sampling if the selection depends on the configuration in a way that is not accounted for. We avoid this pitfall by introducing appropriate auxiliary variables. This results in an implementation that is closely related to "configurational freezing" and "elastic barrier dynamical freezing." We implement the method and validate that it can be used to supplement conventional molecular dynamics in free energy calculations (absolute hydration and relative binding).
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Affiliation(s)
- Joshua Fass
- Computation, Relay Therapeutics, Cambridge, Massachusetts 02139, United States
| | - Forrest York
- Computation, Relay Therapeutics, Cambridge, Massachusetts 02139, United States
| | - Matthew Wittmann
- Computation, Relay Therapeutics, Cambridge, Massachusetts 02139, United States
| | - Joseph Kaus
- Computation, Relay Therapeutics, Cambridge, Massachusetts 02139, United States
| | - Yutong Zhao
- Computation, Relay Therapeutics, Cambridge, Massachusetts 02139, United States
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2
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Lim NM, Osato M, Warren GL, Mobley DL. Fragment Pose Prediction Using Non-equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations. J Chem Theory Comput 2020; 16:2778-2794. [PMID: 32167763 PMCID: PMC7325745 DOI: 10.1021/acs.jctc.9b01096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Part of early stage drug discovery involves determining how molecules may bind to the target protein. Through understanding where and how molecules bind, chemists can begin to build ideas on how to design improvements to increase binding affinities. In this retrospective study, we compare how computational approaches like docking, molecular dynamics (MD) simulations, and a non-equilibrium candidate Monte Carlo (NCMC)-based method (NCMC + MD) perform in predicting binding modes for a set of 12 fragment-like molecules, which bind to soluble epoxide hydrolase. We evaluate each method's effectiveness in identifying the dominant binding mode and finding additional binding modes (if any). Then, we compare our predicted binding modes to experimentally obtained X-ray crystal structures. We dock each of the 12 small molecules into the apo-protein crystal structure and then run simulations up to 1 μs each. Small and fragment-like molecules likely have smaller energy barriers separating different binding modes by virtue of relatively fewer and weaker interactions relative to drug-like molecules and thus likely undergo more rapid binding mode transitions. We expect, thus, to see more rapid transitions between binding modes in our study. Following this, we build Markov State Models to define our stable ligand binding modes. We investigate if adequate sampling of ligand binding modes and transitions between them can occur at the microsecond timescale using traditional MD or a hybrid NCMC+MD simulation approach. Our findings suggest that even with small fragment-like molecules, we fail to sample all the crystallographic binding modes using microsecond MD simulations, but using NCMC+MD, we have better success in sampling the crystal structure while obtaining the correct populations.
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Affiliation(s)
- Nathan M Lim
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California 92697, United States
| | - Meghan Osato
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California 92697, United States
| | - Gregory L Warren
- OpenEye Scientific Software, Santa Fe, New Mexico 87508, United States
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California-Irvine, Irvine, California 92697, United States
- Department of Chemistry, University of California-Irvine, Irvine, California 92697, United States
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3
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Gill SC, Lim NM, Grinaway PB, Rustenburg AS, Fass J, Ross GA, Chodera JD, Mobley DL. Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo. J Phys Chem B 2018; 122:5579-5598. [PMID: 29486559 PMCID: PMC5980761 DOI: 10.1021/acs.jpcb.7b11820] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Accurately predicting protein-ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This problem is important in its own right, but is even more timely given the recent success of alchemical free energy calculations. Alchemical calculations are increasingly used to predict binding free energies of ligands to receptors. However, the accuracy of these calculations is dependent on proper sampling of the relevant ligand binding modes. Unfortunately, ligand binding modes may often be uncertain, hard to predict, and/or slow to interconvert on simulation time scales, so proper sampling with current techniques can require prohibitively long simulations. We need new methods which dramatically improve sampling of ligand binding modes. Here, we develop and apply a nonequilibrium candidate Monte Carlo (NCMC) method to improve sampling of ligand binding modes. In this technique, the ligand is rotated and subsequently allowed to relax in its new position through alchemical perturbation before accepting or rejecting the rotation and relaxation as a nonequilibrium Monte Carlo move. When applied to a T4 lysozyme model binding system, this NCMC method shows over 2 orders of magnitude improvement in binding mode sampling efficiency compared to a brute force molecular dynamics simulation. This is a first step toward applying this methodology to pharmaceutically relevant binding of fragments and, eventually, drug-like molecules. We are making this approach available via our new Binding modes of ligands using enhanced sampling (BLUES) package which is freely available on GitHub.
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Affiliation(s)
- Samuel C. Gill
- Department of Chemistry, University of California, Irvine
| | - Nathan M. Lim
- Department of Pharmaceutical Sciences, University of California, Irvine
| | - Patrick B. Grinaway
- Graduate Program in Physiology, Biophysics, and Systems Biology, Weill Cornell Medical College, New York, NY 10065
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Ariën S. Rustenburg
- Graduate Program in Physiology, Biophysics, and Systems Biology, Weill Cornell Medical College, New York, NY 10065
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Josh Fass
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Tri-Institutional PhD Program in Computational Biology and Medicine, New York, NY 10065
| | - Gregory A. Ross
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | | | - David L. Mobley
- Department of Chemistry, University of California, Irvine
- Department of Pharmaceutical Sciences, University of California, Irvine
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4
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Kurut A, Fonseca R, Boomsma W. Driving Structural Transitions in Molecular Simulations Using the Nonequilibrium Candidate Monte Carlo. J Phys Chem B 2018; 122:1195-1204. [PMID: 29260565 DOI: 10.1021/acs.jpcb.7b11426] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hybrid simulation procedures which combine molecular dynamics with Monte Carlo are attracting increasing attention as tools for improving the sampling efficiency in molecular simulations. In particular, encouraging results have been reported for nonequilibrium candidate protocols, in which a Monte Carlo move is applied gradually, and interleaved with a process that equilibrates the remaining degrees of freedom. Although initial studies have uncovered a substantial potential of the method, its practical applicability for sampling structural transitions in macromolecules remains incompletely understood. Here, we address this issue by systematically investigating the efficiency of the nonequilibrium candidate Monte Carlo on the sampling of rotameric distributions of two peptide systems at atomistic resolution both in vacuum and explicit solvent. The studied systems allow us to directly probe the efficiency with which a single or a few slow degrees of freedom can be driven between well-separated free-energy minima and to explore the sensitivity of the method toward the involved free parameters. In line with results on other systems, our study suggests that order-of-magnitude gains can be obtained in certain scenarios but also identifies challenges that arise when applying the procedure in explicit solvent.
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Affiliation(s)
- Anıl Kurut
- Department of Computer Science, University of Copenhagen , 2100 Copenhagen Ø, Denmark
| | - Rasmus Fonseca
- Department of Molecular and Cellular Physiology, Stanford University , Stanford, California 94305, United States
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen , 2100 Copenhagen Ø, Denmark
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5
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Giovannelli E, Cardini G, Chelli R. Simulations in generalized ensembles through noninstantaneous switches. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:043310. [PMID: 26565367 DOI: 10.1103/physreve.92.043310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Indexed: 06/05/2023]
Abstract
Generalized-ensemble simulations, such as replica exchange and serial generalized-ensemble methods, are powerful simulation tools to enhance sampling of free energy landscapes in systems with high energy barriers. In these methods, sampling is enhanced through instantaneous transitions of replicas, i.e., copies of the system, between different ensembles characterized by some control parameter associated with thermodynamical variables (e.g., temperature or pressure) or collective mechanical variables (e.g., interatomic distances or torsional angles). An interesting evolution of these methodologies has been proposed by replacing the conventional instantaneous (trial) switches of replicas with noninstantaneous switches, realized by varying the control parameter in a finite time and accepting the final replica configuration with a Metropolis-like criterion based on the Crooks nonequilibrium work (CNW) theorem. Here we revise these techniques focusing on their correlation with the CNW theorem in the framework of Markovian processes. An outcome of this report is the derivation of the acceptance probability for noninstantaneous switches in serial generalized-ensemble simulations, where we show that explicit knowledge of the time dependence of the weight factors entering such simulations is not necessary. A generalized relationship of the CNW theorem is also provided in terms of the underlying equilibrium probability distribution at a fixed control parameter. Illustrative calculations on a toy model are performed with serial generalized-ensemble simulations, especially focusing on the different behavior of instantaneous and noninstantaneous replica transition schemes.
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Affiliation(s)
- Edoardo Giovannelli
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Gianni Cardini
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Riccardo Chelli
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
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6
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Giovannelli E, Cardini G, Gellini C, Pietraperzia G, Chelli R. Computing Free Energy Differences of Configurational Basins. J Chem Theory Comput 2015; 11:3561-71. [DOI: 10.1021/acs.jctc.5b00248] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Edoardo Giovannelli
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Gianni Cardini
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
- European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy
| | - Cristina Gellini
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
- European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy
| | - Giangaetano Pietraperzia
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
- European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy
| | - Riccardo Chelli
- Dipartimento
di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
- European Laboratory for Nonlinear Spectroscopy (LENS), Via Nello Carrara 1, I-50019 Sesto Fiorentino, Italy
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7
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Giovannelli E, Cardini G, Gellini C, Pietraperzia G, Chelli R. Annealed importance sampling with constant cooling rate. J Chem Phys 2015; 142:074102. [PMID: 25701997 DOI: 10.1063/1.4907883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Annealed importance sampling is a simulation method devised by Neal [Stat. Comput. 11, 125 (2001)] to assign weights to configurations generated by simulated annealing trajectories. In particular, the equilibrium average of a generic physical quantity can be computed by a weighted average exploiting weights and estimates of this quantity associated to the final configurations of the annealed trajectories. Here, we review annealed importance sampling from the perspective of nonequilibrium path-ensemble averages [G. E. Crooks, Phys. Rev. E 61, 2361 (2000)]. The equivalence of Neal's and Crooks' treatments highlights the generality of the method, which goes beyond the mere thermal-based protocols. Furthermore, we show that a temperature schedule based on a constant cooling rate outperforms stepwise cooling schedules and that, for a given elapsed computer time, performances of annealed importance sampling are, in general, improved by increasing the number of intermediate temperatures.
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Affiliation(s)
- Edoardo Giovannelli
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Gianni Cardini
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Cristina Gellini
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Giangaetano Pietraperzia
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
| | - Riccardo Chelli
- Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, I-50019 Sesto Fiorentino, Italy
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8
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Zerbetto M, Frezzato D. Towards bulk thermodynamics via non-equilibrium methods: gaseous methane as a case study. Phys Chem Chem Phys 2015; 17:1966-79. [DOI: 10.1039/c4cp03815k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The equation of state of bulk materials is achieved via thermodynamic derivatives of the free energy yielded by nonequilibrium transformations and Jarzynski equality.
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Affiliation(s)
- Mirco Zerbetto
- Dipartimento di Scienze Chimiche
- Università degli Studi di Padova
- I-35131 Padova
- Italy
| | - Diego Frezzato
- Dipartimento di Scienze Chimiche
- Università degli Studi di Padova
- I-35131 Padova
- Italy
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