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Relative binding free energy calculations with transformato: A molecular dynamics engine-independent tool

Johannes Karwounopoulos, Marcus Wieder, Stefan Boresch
2022 Frontiers in Molecular Biosciences  
To validate the method, we calculated 76 relative binding free energy differences ΔΔGL1→L2bind for five protein–ligand systems.  ...  We present the software package transformato for the setup of large-scale relative binding free energy calculations.  ...  Acknowledgments MW is grateful for the support of Thierry Langer, who donated significant computational resources to perform parts of the calculations/simulations.  ... 
doi:10.3389/fmolb.2022.954638 pmid:36148009 pmcid:PMC9485484 fatcat:5k7wjuf4yvgbbhvspaoo4x35hi

CHARMM-GUI PDB Manipulator for Advanced Modeling and Simulations of Proteins Containing Nonstandard Residues [chapter]

Sunhwan Jo, Xi Cheng, Shahidul M. Islam, Lei Huang, Huan Rui, Allen Zhu, Hui Sun Lee, Yifei Qi, Wei Han, Kenno Vanommeslaeghe, Alexander D. MacKerell, Benoît Roux (+1 others)
2014 Advances in Protein Chemistry and Structural Biology  
Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to setup a broad range of simulations including free  ...  energy calculation and large-scale coarse-grained representation.  ...  Acknowledgments We wish to acknowledge the help from Christopher Ahern with the unnatural amino acids, and the help from Eduardo Perozo and Hassane Mchaourab with the spin-labels.  ... 
doi:10.1016/bs.apcsb.2014.06.002 pmid:25443960 pmcid:PMC4739825 fatcat:6uftkftwnjgqthaa3z6e4imoae

CHARMM-GUI 10 years for biomolecular modeling and simulation

Sunhwan Jo, Xi Cheng, Jumin Lee, Seonghoon Kim, Sang-Jun Park, Dhilon S. Patel, Andrew H. Beaven, Kyu Il Lee, Huan Rui, Soohyung Park, Hui Sun Lee, Benoît Roux (+4 others)
2016 Journal of Computational Chemistry  
Acknowledgments The CHARMM-GUI development has been support in part by grants from NSF MCB-0918374, MCB-1157677, MCB-1516154, DBI-1145987, DBI-1561372, IIA-1359530 (to WI), MCB-1149187, DBI-1145652 (to  ...  Parts of simulations were performed using the Extreme Science and Engineering Discovery Environment (XSEDE) allocations: MCB070009 (to WI) and MCB-100139 (to JBK), which are supported by NSF ACI-1053575  ...  Ligand Binder [86] provides the standardized CHARMM input files for calculations of absolute binding free energies using FEP/MD simulations.  ... 
doi:10.1002/jcc.24660 pmid:27862047 pmcid:PMC5403596 fatcat:anorbwwis5gjhitmjrwwiw3ij4

PBEQ-Solver for online visualization of electrostatic potential of biomolecules

Sunhwan Jo, Miklos Vargyas, Judit Vasko-Szedlar, Benoît Roux, Wonpil Im
2008 Nucleic Acids Research  
PBEQ-Solver calculates (i) electrostatic potential and solvation free energy, (ii) protein-protein (DNA or RNA) electrostatic interaction energy and (iii) pKa of a selected titratable residue.  ...  Marvin-Space molecular visualization software, a Java applet integrated within CHARMM-GUI (http:// www.charmm-gui.org).  ...  ACKNOWLEDGEMENTS The authors are grateful to Martin Karplus for his support, to Nathan Baker for sharing useful information and to Michael Feig for sharing the results of other PB programs.  ... 
doi:10.1093/nar/gkn314 pmid:18508808 pmcid:PMC2447802 fatcat:luwhnyifnvdjtm7mlizlacmelm

Accurate PDZ/Peptide Binding Specificity with Additive and Polarizable Free Energy Simulations

Nicolas Panel, Francesco Villa, Ernesto J. Fuentes, Thomas Simonson
2018 Biophysical Journal  
Four of the ionic mutations were also simulated with the polarizable Drude force field, which represents the first test of this force field for protein/ligand binding free energy changes.  ...  We used free energy perturbation (FEP) to characterize the binding energetics of one wild-type and 17 mutant complexes by simulating 21 alchemical transformations between pairs of complexes.  ...  ACKNOWLEDGMENTS Some of the calculations were done at the CINES and TGCC supercomputer centers of the French computing agency GENCI.  ... 
doi:10.1016/j.bpj.2018.01.008 pmid:29539396 pmcid:PMC5883551 fatcat:7z7ro6dtsnfgfk3tjlinq37rga

Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual Topology Free Energy Perturbation Approach in NAMD

Wei Jiang, Christophe Chipot, Benoît Roux
2019 Journal of Chemical Information and Modeling  
An effective hybrid single-dual-topology protocol is designed for the calculation of relative binding affinities of small ligands to a receptor.  ...  Following this formulation, a set of illustrative calculations of reliable experiment/simulation data, including relative solvation free energies of small molecules and relative binding affinities of drug  ...  Department of Energy.  ... 
doi:10.1021/acs.jcim.9b00362 pmid:31411473 pmcid:PMC7007809 fatcat:y5dwhiy3kfapbp3d2yi3fdvnba

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

Leela S. Dodda, Israel Cabeza de Vaca, Julian Tirado-Rives, William L. Jorgensen
2017 Nucleic Acids Research  
This server has high value for researchers interested in studying any phenomena based on intermolecular interactions with ligands via molecular mechanics simulations.  ...  The LigParGen web server provides an intuitive interface for generating OPLS-AA/1.14*CM1A(-LBCC) force field parameters for organic ligands, in the formats of commonly used molecular dynamics and Monte  ...  their experience with the LigParGen server.  ... 
doi:10.1093/nar/gkx312 pmid:28444340 pmcid:PMC5793816 fatcat:xw6f7o77offvfm5vmz4mkiarhq

The Dynamic Process of Drug–GPCR Binding at Either Orthosteric or Allosteric Sites Evaluated by Metadynamics [chapter]

Sebastian Schneider, Davide Provasi, Marta Filizola
2015 Msphere  
Here, we describe a metadynamics-based approach to study the dynamic process of ligand binding to/unbinding from GPCRs with a higher level of accuracy and yet satisfying efficiency.  ...  This dramatic increase in GPCR structural information has underscored the use of automated docking algorithms for the discovery of novel ligands that can eventually be developed into improved therapeutics  ...  Acknowledgments Funding for this work was provided by National Institutes of Health grants DA026434 and DA034049.  ... 
doi:10.1007/978-1-4939-2914-6_18 pmid:26260607 pmcid:PMC4703114 fatcat:riyvg65ucvd5djgsylmakbi23a

Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations

Anna Pavlova, Jerry M. Parks, James C. Gumbart
2018 Journal of Chemical Theory and Computation  
In comparison to previous CHARMM-compatible parameters for cobalamin we observe a better agreement for the fold angle and lower RMSD in the cobalamin binding site.  ...  Here, we report CHARMM-compatible force field parameters for several corrinoids developed from quantum mechanical calculations.  ...  binding free energies for aquacobalamin. 65 Here, we followed a similar approach in which we computed interaction energies with the PBE density functional.  ... 
doi:10.1021/acs.jctc.7b01236 pmid:29334459 pmcid:PMC5980237 fatcat:mp6ewroaizegvc32ukykazuhi4

Automated docking refinement and virtual compound screening with absolute binding free energy calculations [article]

Germano Heinzelmann, Michael K. Gilson
2020 bioRxiv   pre-print
Here, we introduce the software BAT.py, a Python tool that invokes the AMBER simulation package to fully automate the calculation of binding free energies for a protein with a series of ligands.  ...  AbstractAbsolute binding free energy calculations with explicit solvent molecular simulations can provide estimates of protein-ligand affinities, and thus reduce the time and costs needed to find new drug  ...  Acknowledgement GH thanks FAPESC and CNPq for the research grants. MKG acknowledges funding from National Institute of General Medical Sciences (Grant number GM061300).  ... 
doi:10.1101/2020.04.15.043240 fatcat:ul5usjimcbfpdm72gf5tewcrr4

Probing Carbohydrate Product Expulsion from a Processive Cellulase with Multiple Absolute Binding Free Energy Methods

Lintao Bu, Gregg T. Beckham, Michael R. Shirts, Mark R. Nimlos, William S. Adney, Michael E. Himmel, Michael F. Crowley
2011 Journal of Biological Chemistry  
The calculated binding free energies, ؊14.4 kcal/mol using SMD and ؊11.2 kcal/mol using FEP/MD, are in good qualitative agreement.  ...  using two different approaches: steered molecular dynamics (SMD) simulations and alchemical free energy perturbation molecular dynamics (FEP/ MD) simulations.  ...  Acknowledgments-We thank Larry Taylor and James Matthews for helpful discussions.  ... 
doi:10.1074/jbc.m110.212076 pmid:21454590 pmcid:PMC3093888 fatcat:pmv7pgj73feqtmseen3dievwya

Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors

Shunzhou Wan, Andrew Potterton, Fouad S. Husseini, David W. Wright, Alexander Heifetz, Maciej Malawski, Andrea Townsend-Nicholson, Peter V. Coveney
2020 Interface Focus  
Our predicted binding free energies, calculated using ESMACS, show a good correlation with previously reported experimental values of the ligands studied.  ...  Relative binding free energies, calculated using TIES, accurately predict experimentally determined values within a mean absolute error of approximately 1 kcal mol −1 .  ...  We acknowledge the Leibniz Supercomputing Centre (LRZ) for providing access to SuperMUC, the Poznan Super Computing and Network Centre (PSNC) for providing access to Eagle, Cyfronet in Kraków for providing  ... 
doi:10.1098/rsfs.2019.0128 pmid:33178414 pmcid:PMC7653344 fatcat:aqsnmrxsujcutfmec26k7w53ai

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset

Michael R. Shirts, Christoph Klein, Jason M. Swails, Jian Yin, Michael K. Gilson, David L. Mobley, David A. Case, Ellen D. Zhong
2016 Journal of Computer-Aided Molecular Design  
We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular  ...  run with program-specific default simulation parameter values.  ...  , partition coefficients, and binding free energies, for a range of both model and more realistic systems.  ... 
doi:10.1007/s10822-016-9977-1 pmid:27787702 pmcid:PMC5581938 fatcat:jwygjndeubckvhqm6d7c6nkmgm

A Guide to the Continuous Constant pH Molecular Dynamics Methods in Amber and CHARMM [Article v1.0]

Jack A. Henderson, Ruibin Lui, Julie A. Harris, Yandong Huang, Vinicius M. de Oliviera, Jana Shen
2022 Living journal of computational molecular science  
We thank Zhi (Shane) Yue for contributing the input files for the membrane-enabled hybrid-solvent CpHMD simulations.  ...  We thank Paween Mahinthichaichan for providing comments on the input files for the membrane-enabled hybrid-solvent CpHMD simulations.  ...  D, renin, induced protonation state change of the in- plasmepsin D hibitor; pH-dependent conformational dynamics; proton-coupled dynamics of binding site water; pH-dependent inhibitor binding free energy  ... 
doi:10.33011/livecoms.4.1.1563 fatcat:socrgdwcsndqjj47ymthfz4hi4

Identifying the Hot Spot Residues of the SARS-CoV-2 Main Protease Using MM-PBSA and Multiple Force Fields

Jinyoung Byun, Juyong Lee
2021 Life  
We performed MD simulations with 100 ns for 11 protein–ligand complexes.  ...  To benchmark the influence of various force fields on hot spot residue identification and binding free energy calculation, we performed MD simulations followed by MM-PBSA analysis with three different  ...  • Preparing systems with CHARMM36 force field (c36) The parameter and topology files of complexes were generated from CHARMM-GUI [52] with c36 [33] .  ... 
doi:10.3390/life12010054 pmid:35054447 pmcid:PMC8779590 fatcat:vmss2rcwy5fi5kl2yauxhyc3uy
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