Zobrazeno 1 - 10
of 11
pro vyhledávání: '"Samarjeet Prasad"'
Antimicrobial peptides (AMPs) have been proposed as a potential solution against multiresistant pathogens. Designing novel AMPs requires exploration of a vast chemical space which makes it a challenging problem. Recently natural language processing a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::bbe5fc42cd9fc47de7f7b1eb0da5ddbd
https://doi.org/10.1101/2022.07.08.499340
https://doi.org/10.1101/2022.07.08.499340
Publikováno v:
J Chem Phys
Finding a low dimensional representation of data from long-timescale trajectories of biomolecular processes, such as protein folding or ligand–receptor binding, is of fundamental importance, and kinetic models, such as Markov modeling, have proven
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::77cc27d380a77e8596051d217adf5079
http://arxiv.org/abs/2201.04609
http://arxiv.org/abs/2201.04609
Autor:
Phillip S. Hudson, Félix Aviat, Rubén Meana-Pañeda, Luke Warrensford, Benjamin C. Pollard, Samarjeet Prasad, Michael R. Jones, H. Lee Woodcock, Bernard R. Brooks
Publikováno v:
Journal of computer-aided molecular design. 36(4)
Accurately predicting free energy differences is essential in realizing the full potential of rational drug design. Unfortunately, high levels of accuracy often require computationally expensive QM/MM Hamiltonians. Fortuitously, the cost of employing
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0ace41a61bcb78222b4dac9d8ce1fa37
https://pubmed.ncbi.nlm.nih.gov/35597880
https://pubmed.ncbi.nlm.nih.gov/35597880
Variational embedding of protein folding simulations using gaussian mixture variational autoencoders
Publikováno v:
J Chem Phys
Conformational sampling of biomolecules using molecular dynamics simulations often produces large amount of high dimensional data that makes it difficult to interpret using conventional analysis techniques. Dimensionality reduction methods are thus r
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0affc976cb351160b4116c337fd2a663
http://arxiv.org/abs/2108.12493
http://arxiv.org/abs/2108.12493
Publikováno v:
Journal of computational chemistryREFERENCES. 42(19)
The Eighth-Shell method for parallelization of molecular dynamics simulations has previously been shown to be the most optimal for efficiency at large process counts. However, in its current formulation only the P1 space group is supported for period
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3cbe0a846a5e39ea48a0d882516713ad
https://pubmed.ncbi.nlm.nih.gov/33977553
https://pubmed.ncbi.nlm.nih.gov/33977553
Autor:
Andrea Rizzi, Samarjeet Prasad, David F. Hahn, Levi N. Naden, Maximilian Kuhn, Bryce K. Allen, Hannah E. Bruce Macdonald, Huafeng Xu, Antonia S. J. S. Mey, Julien Michel, Michael R. Shirts, John D. Chodera, David L. Mobley, Gary Tresadern, Jenke Scheen
Publikováno v:
Living journal of computational molecular science, vol 2, iss 1
Living J Comput Mol Sci
Living J Comput Mol Sci
Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark of these methods is the use of “bridging” potential energy functi
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8a542770ba03c8a1dc2804068986cd9b
https://escholarship.org/uc/item/87m6x1sw
https://escholarship.org/uc/item/87m6x1sw
Publikováno v:
Biophysical Journal. 121:286a
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::01ab093aa47925cb8c9f8e23a98396f6
https://doi.org/10.1016/j.bpj.2021.11.1314
https://doi.org/10.1016/j.bpj.2021.11.1314
Publikováno v:
Journal of Computer-Aided Molecular Design. 32:1191-1201
In this work we have developed a hybrid QM and MM approach to predict pKa of small drug-like molecules in explicit solvent. The gas phase free energy of deprotonation is calculated using the M06–2X density functional theory level with Pople basis s
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3a96e888609edb41d126e8d62cb550f0
https://doi.org/10.1007/s10822-018-0167-1
https://doi.org/10.1007/s10822-018-0167-1
Autor:
Samarjeet Prasad, Bernard R. Brooks
Publikováno v:
J Comput Aided Mol Des
Water octanol partition coefficient serves as a measure for the lipophilicity of a molecule and is important in the field of drug discovery. A novel method for computational prediction of logarithm of partition coefficient (logP) has been developed u
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2425d5444b66b3f84e7d3133d7fb7d63
https://pubmed.ncbi.nlm.nih.gov/32002779
https://pubmed.ncbi.nlm.nih.gov/32002779
Autor:
David L. Mobley, Heather B. Mayes, Justin B. Gilmer, Samarjeet Prasad, Jacob I. Monroe, Daniel M. Zuckerman, Efrem Braun
Publikováno v:
Living Journal of Computational Molecular Science. 1
This document provides a starting point for approaching molecular simulations, guiding beginning practitioners to what issues they need to know about before and while starting their first simulations, and why those issues are so critical. This docume
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8b694447b793df1587376221838ea667
https://doi.org/10.33011/livecoms.1.1.5957
https://doi.org/10.33011/livecoms.1.1.5957