Zobrazeno 1 - 10
of 29
pro vyhledávání: '"Kate A. Stafford"'
Autor:
Kate A. Stafford, Arthur G. Palmer III
Publikováno v:
F1000Research, Vol 3 (2014)
Ribonuclease H1 (RNase H) enzymes are well-conserved endonucleases that are present in all domains of life and are particularly important in the life cycle of retroviruses as domains within reverse transcriptase. Despite extensive study, especially o
Externí odkaz:
https://doaj.org/article/9bd53528e7df4ec8940eb889cbbf3681
Publikováno v:
Journal of chemical information and modeling, vol 62, iss 5
Structure-based, virtual High-Throughput Screening (vHTS) methods for predicting ligand activity in drug discovery are important when there are no or relatively few known compounds that interact with a therapeutic target of interest. State-of-the-art
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::baaca5c81685cf7b70b816258cfbf346
https://pubmed.ncbi.nlm.nih.gov/35235748
https://pubmed.ncbi.nlm.nih.gov/35235748
Structure-based, virtual High Throughput Screening (vHTS) methods for predicting ligand activity in drug discovery are important when there are no or relatively few known compounds that interact with a therapeutic target of interest. State-of-the-art
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1d393e429311af04f92fbc72de04f1f4
https://doi.org/10.26434/chemrxiv-2021-t6xkj
https://doi.org/10.26434/chemrxiv-2021-t6xkj
Publikováno v:
Journal of Chemical Theory and Computation. 12:2489-2492
Thermodynamic stability is a central requirement for protein function, and one goal of protein engineering is improvement of stability, particularly for applications in biotechnology. Herein, molecular dynamics simulations are used to predict in vitr
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9472fc35247e67dd3fe551617e391fe5
https://doi.org/10.1021/acs.jctc.6b00120
https://doi.org/10.1021/acs.jctc.6b00120
Autor:
Arthur G. Palmer, Joel A. Butterwick, Richard A. Friesner, Robert Abel, Nikola Trbovic, Kate A. Stafford
Publikováno v:
Journal of Molecular Biology. 427:853-866
The conformational basis for reduced activity of the thermophilic ribonuclease HI enzyme from Thermus thermophilus, compared to its mesophilic homolog from Escherichia coli, is elucidated using a combination of NMR spectroscopy and molecular dynamics
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1d35c94e10d1ad5fee7c9427ce438866
https://doi.org/10.1016/j.jmb.2014.11.023
https://doi.org/10.1016/j.jmb.2014.11.023
Publikováno v:
Proteins: Structure, Function, and Bioinformatics. 81:499-509
Factors affecting the accuracy of molecular dynamics (MD) simulations are investigated by comparing generalized order parameters for backbone NH vectors of the B3 immunoglobulin-binding domain of streptococcal protein G (GB3) derived from simulations
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::76eb2c92aab6b6f6326e3636108fa5a7
https://doi.org/10.1002/prot.24209
https://doi.org/10.1002/prot.24209
Publikováno v:
Journal of the American Chemical Society. 134:6365-6374
In this investigation, semiempirical NMR chemical shift prediction methods are used to evaluate the dynamically averaged values of backbone chemical shifts obtained from unbiased molecular dynamics (MD) simulations of proteins. MD-averaged chemical s
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3d7f1fef845e027b977c3916e346b41c
https://doi.org/10.1021/ja300265w
https://doi.org/10.1021/ja300265w
Autor:
Kate A. Stafford, Paul Maragakis, Justin Gullingsrud, Yibing Shan, Stefano Piana, Patrick J. Miller, Michael P. Eastwood, C. A. Rendleman, Willy Wriggers, Kresten Lindorff-Larsen, David E. Shaw, Ron O. Dror
Publikováno v:
Journal of Chemical Theory and Computation. 5:2595-2605
Events of scientific interest in molecular dynamics (MD) simulations, including conformational changes, folding transitions, and translocations of ligands and reaction products, often correspond to high-level structural rearrangements that alter cont
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::32fd70d472ea5b058a6c689d746e37a9
https://doi.org/10.1021/ct900229u
https://doi.org/10.1021/ct900229u
Autor:
Michael P. Eastwood, Ron O. Dror, David E. Shaw, Kate A. Stafford, Cristian Predescu, Ross A. Lippert, Morten Ø. Jensen, Paul Maragakis
Publikováno v:
Journal of chemical theory and computation. 6(7)
Since the behavior of biomolecules can be sensitive to temperature, the ability to accurately calculate and control the temperature in molecular dynamics (MD) simulations is important. Standard analysis of equilibrium MD simulations-even constant-ene
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::6e1166aa84544cf6fe953f90bf9eca29
https://pubmed.ncbi.nlm.nih.gov/26615934
https://pubmed.ncbi.nlm.nih.gov/26615934
Publikováno v:
Journal of the American Chemical Society
Journal of the American Chemical Society, American Chemical Society, 2013, 135 (48), pp.18024-18027. ⟨10.1021/ja409479y⟩
Journal of the American Chemical Society, 2013, 135 (48), pp.18024-18027. ⟨10.1021/ja409479y⟩
Journal of the American Chemical Society, American Chemical Society, 2013, 135 (48), pp.18024-18027. ⟨10.1021/ja409479y⟩
Journal of the American Chemical Society, 2013, 135 (48), pp.18024-18027. ⟨10.1021/ja409479y⟩
International audience; : Many proteins use Asx and Glx (x = n, p, or u) side chains as key functional groups in enzymatic catalysis and molecular recognition. In this study, NMR spin relaxation experiments and molecular dynamics (MD) simulations are
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::057ec9b1ca54faf4352adf25d38e243b
https://europepmc.org/articles/PMC3918730/
https://europepmc.org/articles/PMC3918730/