Zobrazeno 1 - 10
of 210
pro vyhledávání: '"Bruce R, Donald"'
Autor:
Valentina Kugler, Andreas Lieb, Nathan Guerin, Bruce R. Donald, Eduard Stefan, Teresa Kaserer
Publikováno v:
Communications Biology, Vol 6, Iss 1, Pp 1-6 (2023)
Abstract We report an Osprey-based computational protocol to prospectively identify oncogenic mutations that act via disruption of molecular interactions. It is applicable to analyse both protein-protein and protein-DNA interfaces and it is validated
Externí odkaz:
https://doaj.org/article/44c54c3e1e4348bb8e98e527dd1bde73
Publikováno v:
Journal of Structural Biology: X, Vol 8, Iss , Pp 100091- (2023)
Podisus maculiventris thanatin has been reported as a potent antimicrobial peptide with antibacterial and antifungal activity. Its antibiotic activity has been most thoroughly characterized against E. coli and shown to interfere with multiple pathway
Externí odkaz:
https://doaj.org/article/869502dddc7f43d58e74bd1eb504799b
Autor:
Graham T. Holt, Jason Gorman, Siyu Wang, Anna U. Lowegard, Baoshan Zhang, Tracy Liu, Bob C. Lin, Mark K. Louder, Marcel S. Frenkel, Krisha McKee, Sijy O’Dell, Reda Rawi, Chen-Hsiang Shen, Nicole A. Doria-Rose, Peter D. Kwong, Bruce R. Donald
Publikováno v:
Cell Reports, Vol 42, Iss 7, Pp 112711- (2023)
Summary: Broadly neutralizing antibodies (bNAbs) against HIV can reduce viral transmission in humans, but an effective therapeutic will require unusually high breadth and potency of neutralization. We employ the OSPREY computational protein design so
Externí odkaz:
https://doaj.org/article/7bf365dbc2d84edd9523bc03a999144f
Publikováno v:
STAR Protocols, Vol 4, Iss 2, Pp 102170- (2023)
Summary: Prospective predictions of drug-resistant protein mutants could improve the design of therapeutics less prone to resistance. Here, we describe RESISTOR, an algorithm that uses structure- and sequence-based criteria to predict resistance muta
Externí odkaz:
https://doaj.org/article/df344fed3a654445bfa3fdf244d3ff39
Autor:
Siyu Wang, Stephanie M Reeve, Graham T Holt, Adegoke A Ojewole, Marcel S Frenkel, Pablo Gainza, Santosh Keshipeddy, Vance G Fowler, Dennis L Wright, Bruce R Donald
Publikováno v:
PLoS Computational Biology, Vol 18, Iss 2, p e1009855 (2022)
Antimicrobial resistance presents a significant health care crisis. The mutation F98Y in Staphylococcus aureus dihydrofolate reductase (SaDHFR) confers resistance to the clinically important antifolate trimethoprim (TMP). Propargyl-linked antifolates
Externí odkaz:
https://doaj.org/article/760112bcadb84e1a84002595002ee2fb
Autor:
Bruce R. Donald
An overview of algorithms important to computational structural biology that addresses such topics as NMR and design and analysis of proteins.Using the tools of information technology to understand the molecular machinery of the cell offers both chal
Publikováno v:
Journal of Computational Biology. 29:1346-1352
Autor:
Anna U Lowegard, Marcel S Frenkel, Graham T Holt, Jonathan D Jou, Adegoke A Ojewole, Bruce R Donald
Publikováno v:
PLoS Computational Biology, Vol 16, Iss 6, p e1007447 (2020)
The K* algorithm provably approximates partition functions for a set of states (e.g., protein, ligand, and protein-ligand complex) to a user-specified accuracy ε. Often, reaching an ε-approximation for a particular set of partition functions takes
Externí odkaz:
https://doaj.org/article/f824df9242644807b55d5143527212cf
Publikováno v:
PLoS Computational Biology, Vol 13, Iss 3, p e1005346 (2017)
Protein design algorithms enumerate a combinatorial number of candidate structures to compute the Global Minimum Energy Conformation (GMEC). To efficiently find the GMEC, protein design algorithms must methodically reduce the conformational search sp
Externí odkaz:
https://doaj.org/article/3908321b543544069fe12083525a2d74
Publikováno v:
Journal of Computational Biology. 27:550-564
Protein design algorithms that model continuous sidechain flexibility and conformational ensembles better approximate the in vitro and in vivo behavior of proteins. The previous state of the art, iMinDEE-\(A^*\)-\(K^*\), computes provable \(\varepsil