Y
Yuk Y. Sham
Researcher at University of Minnesota
Publications - 86
Citations - 3720
Yuk Y. Sham is an academic researcher from University of Minnesota. The author has contributed to research in topics: Receptor & Protein folding. The author has an hindex of 29, co-authored 80 publications receiving 3434 citations. Previous affiliations of Yuk Y. Sham include Florida International University & Science Applications International Corporation.
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Consistent Calculations of pKa's of Ionizable Residues in Proteins: Semi-microscopic and Microscopic Approaches
TL;DR: In this paper, the pKa's of ionizable groups in proteins are calculated using the semi-microscopic version of the protein dipoles Langevin dipoles (PDLD) model, which treats the protein relaxation in the microscopic framework of the linear response approximation.
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Blue Gene: a vision for protein science using a petaflop supercomputer
F. E. Allen,George Almási,Wanda Andreoni,D. Beece,Bruce J. Berne,A. A. Bright,Jose R. Brunheroto,Calin Cascaval,José G. Castaños,Paul W. Coteus,Paul G. Crumley,Alessandro Curioni,Monty M. Denneau,Wilm E. Donath,Maria Eleftheriou,Blake G. Fitch,Bruce M. Fleischer,Christos John Georgiou,Robert S. Germain,Mark E. Giampapa,Donna L. Gresh,Manish Gupta,R. A. Haring,H. Ho,Peter H. Hochschild,Susan Flynn Hummel,T. Jonas,Derek Lieber,Glenn J. Martyna,K. Maturu,José E. Moreira,D.M. Newns,M. Newton,Robert Alan Philhower,T. Picunko,Jed W. Pitera,Michael C. Pitman,Rick A. Rand,Ajay K. Royyuru,Valentina Salapura,A. Sanomiya,R. Shah,Yuk Y. Sham,Suryabhan Singh,Marc Snir,Frank Suits,Richard A. Swetz,William C. Swope,N. Vishnumurthy,T.J.C. Ward,Henry S. Warren,Ruhong Zhou +51 more
TL;DR: An overview of the Blue Gene project at IBM Research is provided to advance the understanding of the mechanisms behind protein folding via large-scale simulation, and to explore novel ideas in massively parallel machine architecture and software.
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Examining methods for calculations of binding free energies: LRA, LIE, PDLD‐LRA, and PDLD/S‐LRA calculations of ligands binding to an HIV protease
TL;DR: It is found in the present case that the contribution from the non‐polar states to the protein‐ligand binding energy is rather small, but it is clearly expected that this term is not negligible in cases where the protein provides preorganized environment to stabilize the residual charges of the ligand.
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Structured disorder and conformational selection.
TL;DR: It is proposed that engineering‐optimized specific electrostatic interactions to avoid electrostatic repulsion would reduce the type I disordered state, driving the molten globule → native (N) state, leading to the denatured → MG → N state.
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The effect of protein relaxation on charge-charge interactions and dielectric constants of proteins
TL;DR: An explicit consideration of the protein relaxation leads to a significant increase in epsilon(eff) and that semimicroscopic models that do not take this relaxation into account force one to use a large value for the so-called "protein dielectric constant" of the Poisson-Boltzmann model.