Zobrazeno 1 - 10
of 45
pro vyhledávání: '"Robert B. Murphy"'
Autor:
Kenneth W. Borrelli, Matthew J Grisewood, Phani Ghanakota, Richard A. Friesner, Edward B. Miller, Troast Dawn M, Daniel J. Sindhikara, Robert B. Murphy, Robert Abel, Salma B Rafi, Nicholas A. Boyles, Fabio Ranalli, Tyler Day, Steven V. Jerome, Sayan Mondal, Steven L. Dixon
Publikováno v:
Journal of Chemical Theory and Computation. 17:2630-2639
We present a reliable and accurate solution to the induced fit docking problem for protein-ligand binding by combining ligand-based pharmacophore docking, rigid receptor docking, and protein structure prediction with explicit solvent molecular dynami
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c9c2ac386fda0ec7c01f20f30e7e0228
https://doi.org/10.1021/acs.jctc.1c00136
https://doi.org/10.1021/acs.jctc.1c00136
Autor:
Christopher D. Schmitz, Ramy Farid, Ivan Tubert-Brohman, Robert B. Murphy, Nicholas A. Boyles, Ramakrishna Annabhimoju, Matthew P. Repasky, Jeremy R. Greenwood, Steven V. Jerome, Richard A. Friesner, Robert Abel
Publikováno v:
Journal of medicinal chemistry. 59(9)
We have developed a new methodology for protein–ligand docking and scoring, WScore, incorporating a flexible description of explicit water molecules. The locations and thermodynamics of the waters are derived from a WaterMap molecular dynamics simu
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::066638d2fb98767e22d0d42c05642b09
https://pubmed.ncbi.nlm.nih.gov/27054459
https://pubmed.ncbi.nlm.nih.gov/27054459
Publikováno v:
Journal of chemical theory and computation. 1(2)
We present a methodology for computing the binding energy of molecular dimers based on extrapolation of pseudospectral local second-order Moller-Plesset (MP2), or PS-LMP2, energies to the basis set limit. The extrapolation protocol is based on carryi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::11f0e68d9c97a41a6058b5e3e3cb4435
https://pubmed.ncbi.nlm.nih.gov/26641295
https://pubmed.ncbi.nlm.nih.gov/26641295
Autor:
Robert B. Murphy, Paul C. Sanschagrin, Thomas A. Halgren, Daniel T. Mainz, Matthew P. Repasky, Richard A. Friesner, Jeremy R. Greenwood, Leah L. Frye
Publikováno v:
Journal of Medicinal Chemistry. 49:6177-6196
A novel scoring function to estimate protein-ligand binding affinities has been developed and implemented as the Glide 4.0 XP scoring function and docking protocol. In addition to unique water desolvation energy terms, protein-ligand structural motif
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::18d8a514f2255fa9b1016d0c752939f9
https://doi.org/10.1021/jm051256o
https://doi.org/10.1021/jm051256o
Autor:
Bruce J. Berne, Hege S. Beard, Richard A. Friesner, Wolfgang Damm, Jon R. Maple, Daniel T. Mainz, Matthew P. Repasky, Yixiang X. Cao, Art E. Cho, Ronald M. Levy, Linda Yu Zhang, Ramy Farid, Emilio Gallicchio, Anthony K. Felts, Dean M. Philipp, Jay L. Banks, Thomas A. Halgren, Robert B. Murphy
Publikováno v:
Journal of Computational Chemistry. 26:1752-1780
We provide an overview of the IMPACT molecular mechanics program with an emphasis on recent developments and a description of its current functionality. With respect to core molecular mechanics technologies we include a status report for the fixed ch
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dc1e8b47b287e77a00e4cb37ff8c3b10
https://doi.org/10.1002/jcc.20292
https://doi.org/10.1002/jcc.20292
Autor:
Victor Guallar, Mu-Hyun Baik, Benjamin F. Gherman, Richard A. Friesner, Maria E. Wirstam, Robert B. Murphy, Stephen J. Lippard
Publikováno v:
Coordination Chemistry Reviews. :267-290
Over the past several years, rapid advances in computational hardware, quantum chemical methods, and mixed quantum mechanics/molecular mechanics (QM/MM) techniques have made it possible to model accurately the interaction of ligands with metal-contai
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::02eb6ea8b2e0a8ff70d5d8d4005cc190
https://doi.org/10.1016/s0010-8545(02)00284-9
https://doi.org/10.1016/s0010-8545(02)00284-9
Autor:
Robert B. Murphy, Thijs Beuming, Richard A. Friesner, Byungchan Kim, Robert Abel, Lingle Wang, Dahlia A. Goldfeld
Publikováno v:
The journal of physical chemistry. B. 119(3)
The kappa opioid receptor (KOR) is an important target for pain and depression therapeutics that lack harmful and addictive qualities of existing medications. We present a model for the binding of morphinan ligands and JDTic to the JDTic/KOR crystal
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b5332535a80dae8b7b0d135d99dc8dc3
https://pubmed.ncbi.nlm.nih.gov/25395044
https://pubmed.ncbi.nlm.nih.gov/25395044
Publikováno v:
The Journal of Chemical Physics. 112:10131-10141
Novel improvements of the pseudospectral method for assembling the Coulomb operator are discussed. These improvements consist of a fast atom centered multipole method and a variation of the Head–Gordan J-engine analytic integral evaluation. The det
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::22f83a65baf6d6f793960282880edbc8
https://doi.org/10.1063/1.481704
https://doi.org/10.1063/1.481704
Publikováno v:
Chemical Physics Letters. 321:113-120
We have developed a density functional (DFT) version of our quantum chemistry/molecular mechanics (QM/MM) methodology based on using frozen molecular orbitals as the interface between the QM and MM regions. The methodology is distinguished from previ
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::3bc9967bd738f06637d4451860a7a17d
https://doi.org/10.1016/s0009-2614(00)00289-x
https://doi.org/10.1016/s0009-2614(00)00289-x
Publikováno v:
Journal of Computational Chemistry. 21:1442-1457
A QM–MM method, using our previously developed frozen orbital QM–MM interface methodolgy, is presented as a general, accurate, and computationally efficient model for studying chemical problems in a protein environment. The method, its parametriz
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::b00a59a9728805195acd2c72c3275e7e
https://doi.org/10.1002/1096-987x(200012)21:16<1442::aid-jcc3>3.0.co
https://doi.org/10.1002/1096-987x(200012)21:16<1442::aid-jcc3>3.0.co