Zobrazeno 1 - 10
of 245
pro vyhledávání: '"Michael K, Gilson"'
Publikováno v:
Scientific Reports, Vol 12, Iss 1, Pp 1-11 (2022)
Abstract We determined the effectiveness of absolute binding free energy (ABFE) calculations to refine the selection of active compounds in virtual compound screening, a setting where the more commonly used relative binding free energy approach is no
Externí odkaz:
https://doaj.org/article/3e3fbe7233cc4fc4933b699dcdfbe719
Autor:
Germano Heinzelmann, Michael K. Gilson
Publikováno v:
Scientific Reports, Vol 11, Iss 1, Pp 1-18 (2021)
Abstract Absolute 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 candidates. However, these calculations can
Externí odkaz:
https://doaj.org/article/a364c3436369474ba4dc7d8ed0d515fb
Autor:
Lorillee Tallorin, JiaLei Wang, Woojoo E. Kim, Swagat Sahu, Nicolas M. Kosa, Pu Yang, Matthew Thompson, Michael K. Gilson, Peter I. Frazier, Michael D. Burkart, Nathan C. Gianneschi
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-10 (2018)
The discovery of peptide substrates for enzymes with selective activities is a central goal in chemical biology. Here, the authors develop a hybrid method combining machine learning and experimental testing for fast optimization of peptides for speci
Externí odkaz:
https://doaj.org/article/d9ae7a50ccf5436cb95b497dfe663903
Autor:
Shin-Fu Chen, Nan-Lan Huang, Jung-Hsin Lin, Chyuan-Chuan Wu, Ying-Ren Wang, Yu-Jen Yu, Michael K. Gilson, Nei-Li Chan
Publikováno v:
Nature Communications, Vol 9, Iss 1, Pp 1-13 (2018)
Type II DNA topoisomerases (Top2s) direct the passage of one DNA duplex through another, which is important for resolving DNA entanglements. Here the authors combine X-ray crystallography and MD simulations and present the structure of the human Top2
Externí odkaz:
https://doaj.org/article/658289d67ad24135b29bba4a1384fb23
Autor:
Simon Boothroyd, Pavan Kumar Behara, Owen C. Madin, David F. Hahn, Hyesu Jang, Vytautas Gapsys, Jeffrey R. Wagner, Joshua T. Horton, David L. Dotson, Matthew W. Thompson, Jessica Maat, Trevor Gokey, Lee-Ping Wang, Daniel J. Cole, Michael K. Gilson, John D. Chodera, Christopher I. Bayly, Michael R. Shirts, David L. Mobley
Publikováno v:
Journal of chemical theory and computation, vol 19, iss 11
We introduce the Open Force Field (OpenFF) 2.0.0 small molecule force field for drug-like molecules, code-named Sage, which builds upon our previous iteration, Parsley. OpenFF force fields are based on direct chemical perception, which generalizes ea
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fb71789c7555db802bd690b7ec3bb1ad
https://escholarship.org/uc/item/35b7v1pz
https://escholarship.org/uc/item/35b7v1pz
Autor:
Crystal Nguyen, Takeshi Yamazaki, Andriy Kovalenko, David A Case, Michael K Gilson, Tom Kurtzman, Tyler Luchko
Publikováno v:
PLoS ONE, Vol 14, Iss 7, p e0219473 (2019)
Computed, high-resolution, spatial distributions of solvation energy and entropy can provide detailed information about the role of water in molecular recognition. While grid inhomogeneous solvation theory (GIST) provides rigorous, detailed thermodyn
Externí odkaz:
https://doaj.org/article/9764eb4a73724c5db0cf25ba57afe59d
Autor:
Jehad Almaliti, Pavla Fajtová, Jaeson Calla, Gregory M. LaMonte, Mudong Feng, Frances Rocamora, Sabine Ottilie, Evgenia Glukhov, Evzen Boura, Raymond T. Suhandynata, Jeremiah D. Momper, Michael K. Gilson, Elizabeth A. Winzeler, William H. Gerwick, Anthony J. O'Donoghue
Here we present remarkable epoxyketone-based proteasome inhibitors with low nanomolar in vitro potency for blood-stage Plasmodium falciparum and low cytotoxicity for human cells. Our best compound has more than 2,000-fold greater selectivity for eryt
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=od______2659::b8eb6ef78093603656917035ab9eee71
https://zenodo.org/record/7655290
https://zenodo.org/record/7655290
Publikováno v:
J Chem Theory Comput
Molecular dynamics (MD) simulations of proteins are commonly used to sample from the Boltzmann distribution of conformational states, with wide-ranging applications spanning chemistry, biophysics, and drug discovery. However, MD can be inefficient at
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d4f75844449090aa114878a64484c143
https://doi.org/10.1021/acs.jctc.1c00867
https://doi.org/10.1021/acs.jctc.1c00867
Autor:
Jehad Almaliti, Pavla Fajtová, Jaeson Calla, Gregory M. LaMonte, Mudong Feng, Frances Rocamora, Sabine Ottilie, Evgenia Glukhov, Evzen Boura, Raymond T. Suhandynata, Jeremiah D. Momper, Michael K. Gilson, Elizabeth A. Winzeler, William H. Gerwick, Anthony J. O’Donoghue
Here we present remarkable epoxyketone-based proteasome inhibitors with low nanomolar in vitro potency for blood-stage Plasmodium falciparum and low cytotoxicity for human cells. Our best compound has more than 2,600-fold greater selectivity for eryt
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d3507796f233551f43ba63292f99457c
https://doi.org/10.1101/2022.08.06.502205
https://doi.org/10.1101/2022.08.06.502205
Publikováno v:
J Comput Aided Mol Des
We investigate the binding of native β-cyclodextrin (β-CD) and eight novel β-CD derivatives with two different guest compounds, using isothermal calorimetry (ITC) and 2D NOESY NMR. In all cases, the stoichiometry is 1:1 and binding is exothermic.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0c89936e72fd78cb1d49a50cf9d810df
https://doi.org/10.1007/s10822-020-00350-w
https://doi.org/10.1007/s10822-020-00350-w