Zobrazeno 1 - 10
of 13
pro vyhledávání: '"Marley L, Samways"'
Publikováno v:
ACS Physical Chemistry Au. 2:247-259
Water molecules play important roles in all biochemical processes. Therefore, it is of key importance to obtain information of the structure, dynamics, and thermodynamics of water molecules around proteins. Numerous computational methods have been su
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4a2af618188e5af040f20605bbfa5989
https://doi.org/10.1021/acsphyschemau.1c00052
https://doi.org/10.1021/acsphyschemau.1c00052
Rimantadine Binds to and Inhibits the Influenza A M2 Proton Channel without Enantiomeric Specificity
Autor:
Athina Konstantinidi, William F. DeGrado, Jessica L. Thomaston, Yanmei Hu, Hannah E. Bruce Macdonald, Marley L. Samways, Chunlong Ma, Jonathan W. Essex, Antonios Kolocouris, Jun Wang
Publikováno v:
Biochemistry
The influenza A M2 wild-type (WT) proton channel is the target of the anti-influenza drug rimantadine. Rimantadine has two enantiomers, though most investigations into drug binding and inhibition have used a racemic mixture. Solid-state NMR experimen
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::97622ab623be9c3a5c693688521b7904
https://pubmed.ncbi.nlm.nih.gov/34342217
https://pubmed.ncbi.nlm.nih.gov/34342217
Enhanced Grand Canonical Sampling of Occluded Water Sites Using Nonequilibrium Candidate Monte Carlo
Publikováno v:
Journal of chemical theory and computation, vol 19, iss 3
Water molecules play a key role in many biomolecular systems, particularly when bound at protein-ligand interfaces. However, molecular simulation studies on such systems are hampered by the relatively long time scales over which water exchange betwee
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::29027c9c09b5a890381f15977f8abb22
https://escholarship.org/uc/item/6dh4436c
https://escholarship.org/uc/item/6dh4436c
Water molecules at protein-ligand interfaces are often of significant pharmaceutical interest, owing in part to the entropy which can be released upon the displacement of an ordered water by a therapeutic compound. Protein structures may not, however
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bcc5fa59646c1eb0d1c3ba24e6e254ec
https://eprints.soton.ac.uk/475722/
https://eprints.soton.ac.uk/475722/
Publikováno v:
Chemical Society Reviews. 50:9104-9120
The fundamental importance of water molecules at drug-protein interfaces is now widely recognised and a significant feature in structure-based drug design. Experimental methods for analysing the role of water in drug binding have many challenges, inc
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a8d0d8db86ae7b1c0d3956dc019dff73
https://doi.org/10.1039/d0cs00151a
https://doi.org/10.1039/d0cs00151a
Autor:
Yunhui Ge, David C. Wych, Marley L. Samways, Michael E. Wall, Jonathan W. Essex, David L. Mobley
Publikováno v:
Journal of chemical theory and computation, vol 18, iss 3
J Chem Theory Comput
J Chem Theory Comput
Water often plays a key role in protein structure, molecular recognition, and mediating protein-ligand interactions. Thus, free energy calculations must adequately sample water motions, which often proves challenging in typical MD simulation time sca
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::944a76dc1474176b4d703d3320bc5018
https://eprints.soton.ac.uk/456313/
https://eprints.soton.ac.uk/456313/
Publikováno v:
Free Energy Methods in Drug Discovery: Current State and Future Directions ISBN: 9780841298064
Whilst the quality of force fields and sampling methodologies has improved significantly over the years, along with the accessible lengths of simulations, there still remain a number of factors which limit the reproducibility of relative binding free
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::181d77d39eee392e22192b6910399f1f
https://doi.org/10.1021/bk-2021-1397.ch004
https://doi.org/10.1021/bk-2021-1397.ch004
Autor:
David C. Wych, David L. Mobley, Marley L. Samways, Yunhui Ge, Jonathan W. Essex, Michael E. Wall
1ABSTRACTWater often plays a key role in protein structure, molecular recognition, and mediating protein-ligand interactions. Thus, free energy calculations must adequately sample water motions, which often proves challenging in typical MD simulation
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::6602379128a5a6425fbb68716c6579ca
https://doi.org/10.1101/2021.06.14.448350
https://doi.org/10.1101/2021.06.14.448350
Autor:
William G, Glass, Jonathan W, Essex, Franca, Fraternali, James, Gebbie-Rayet, Irene, Marzuoli, Marley L, Samways, Philip C, Biggin, Syma, Khalid
Publikováno v:
Methods in molecular biology (Clifton, N.J.). 2302
Current computer architectures, coupled with state-of-the-art molecular dynamics simulation software, facilitate the in-depth study of large biomolecular systems at high levels of detail. However, biological phenomena take place at various time and l
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::656d915d820991fc1c49ec4a28a7c2c2
https://pubmed.ncbi.nlm.nih.gov/33877632
https://pubmed.ncbi.nlm.nih.gov/33877632
Autor:
Jonathan W. Essex, Irene Marzuoli, William G. Glass, Philip C. Biggin, James Gebbie-Rayet, Franca Fraternali, Marley L. Samways, Syma Khalid
Publikováno v:
Methods in Molecular Biology ISBN: 9781071613931
Current computer architectures, coupled with state-of-the-art molecular dynamics simulation software, facilitate the in-depth study of large biomolecular systems at high levels of detail. However, biological phenomena take place at various time and l
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::f6733f7251dcd46fe4f4e1647c0ce258
https://doi.org/10.1007/978-1-0716-1394-8_14
https://doi.org/10.1007/978-1-0716-1394-8_14