Zobrazeno 1 - 10
of 66
pro vyhledávání: '"Evangelos A. Coutsias"'
Publikováno v:
The journal of physical chemistry. B, vol 126, iss 32
We describe Crustwater, a statistical mechanical model of nonpolar solvation in water. It treats bulk water using the Cage Water model and introduces a crust, i.e., a solvation shell of coordinated partially structured waters. Crustwater is analytica
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::80e6a74b3cddee54e6dc6e292dfb271c
https://doi.org/10.1021/acs.jpcb.2c02695
https://doi.org/10.1021/acs.jpcb.2c02695
Publikováno v:
J Chem Inf Model
We present an algorithm, QBKR (Quaternary Backbone Kinematic Reconstruction), a fast analytical method for an all-atom backbone reconstruction of proteins and linear or cyclic peptide chains from [Formula: see text] coordinate traces. Unlike previous
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ccce9ab6df121f79ae6be797d9974d17
https://doi.org/10.1021/acs.jcim.1c00453
https://doi.org/10.1021/acs.jcim.1c00453
Publikováno v:
Journal of Computational Chemistry. 42:271-292
The kinematic geometry of protein backbone structures, constrained by either single or multiple hydrogen bonds (H-bonds), possibly in a periodic array, is discussed. These structures include regular secondary structure elements α-helices and β-shee
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::26f1065b07d9dc304d199df0027b6b0e
https://doi.org/10.1002/jcc.26448
https://doi.org/10.1002/jcc.26448
Autor:
Cong Liu, Evangelos A. Coutsias, Ken A. Dill, Sergei Kotelnikov, Andrey Alekseenko, Mikhail Ignatov, Dzmitry Padhorny, Dima Kozakov, Emiliano Brini, Mark Lukin
Publikováno v:
J Comput Aided Mol Des
We describe a new template-based method for docking flexible ligands such as macrocycles to proteins. It combines Monte-Carlo energy minimization on the manifold (MCMM), a fast manifold search method, with BRIKARD for complex flexible ligand searchin
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::106e6931dd1404c95e61783f6d35abdf
https://doi.org/10.1007/s10822-019-00257-1
https://doi.org/10.1007/s10822-019-00257-1
Autor:
Evangelos A. Coutsias, Reza Latifi, Jimmie D. Weaver, Kamaljeet Singh, Christopher J. Fennell, Steve Hartson
Publikováno v:
Chem. 4:124-137
Summary Intramolecular strain is a powerful driving force for rapid and selective chemical reactions, and it is the cornerstone of strain-induced bioconjugation. However, the use of molecules with built-in strain is often complicated as a result of i
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::9322f015f3abf52489de167c86ebdb5a
https://doi.org/10.1016/j.chempr.2017.11.007
https://doi.org/10.1016/j.chempr.2017.11.007
Autor:
Surya V.S.R.K. Pulavarti, Per Jr Greisen, Gabriel J. Rocklin, Colin Correnti, Thomas W. Linsky, David J. Craik, Olivier Cheneval, Lauren Carter, X. Xu, Quentin Kaas, Jason M. Gilmore, Christopher D. Bahl, Po-Ssu Huang, William A. Johnsen, Andrew M. Watkins, David Baker, Vikram Khipple Mulligan, Peta J. Harvey, Richard Bonneau, Thomas Szyperski, Gaurav Bhardwaj, Garry W. Buchko, Evangelos A. Coutsias, James M. Olson, Stephen A. Rettie, Yifan Song, Alexander Eletsky
Publikováno v:
Nature
Naturally occurring, pharmacologically active peptides constrained with covalent crosslinks generally have shapes that have evolved to fit precisely into binding pockets on their targets. Such peptides can have excellent pharmaceutical properties, co
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cf8778c9d2a01f5c0c9930bd5485921c
https://doi.org/10.1038/nature19791
https://doi.org/10.1038/nature19791
Publikováno v:
Journal of chemical theory and computation, vol 12, iss 9
Natural product and synthetic macrocycles are chemically and topologically diverse. An efficient, accurate, and general method for generating macrocycle conformations would enable structure-based design of macrocycle drugs or host-guest complexes. Co
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5c6be53adf2487ed516d0dae09cfc209
https://doi.org/10.1021/acs.jctc.6b00250
https://doi.org/10.1021/acs.jctc.6b00250
Autor:
Kevin Hauser, Miguel Garcia-Diaz, Carlos Simmerling, Bernard Essuman, Yiqing He, Evangelos A. Coutsias
Publikováno v:
Nucleic Acids Research
Transcription factors (TF) can change shape to bind and recognize DNA, shifting the energy landscape from a weak binding, rapid search mode to a higher affinity recognition mode. However, the mechanism(s) driving this conformational change remains un
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::583dbf6c6621f9055623f211fb4542de
https://doi.org/10.1093/nar/gkv1091
https://doi.org/10.1093/nar/gkv1091
Publikováno v:
Journal of computational chemistry. 40(15)
A common approach for comparing the structures of biomolecules or solid bodies is to translate and rotate one structure with respect to the other to minimize the pointwise root-mean-square deviation (RMSD). We present a new, robust numerical algorith
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e7c723457d2e3aa0f512565419341c24
https://pubmed.ncbi.nlm.nih.gov/30828834
https://pubmed.ncbi.nlm.nih.gov/30828834
Publikováno v:
Journal of chemical information and modeling. 57(4)
A general method is presented to characterize the helical properties of potentially irregular helices, such as those found in protein secondary and tertiary structures and nucleic acids. The method was validated using artificial helices with varying
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::73ff1b2a471618046b9df8cc9c66ba53
https://pubmed.ncbi.nlm.nih.gov/28287728
https://pubmed.ncbi.nlm.nih.gov/28287728