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Science (New York, N.Y.)|October 23, 1998
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solutionY Duan, P A KollmanProceedings of the National Academy of Sciences of the United States of America|August 26, 1998
The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulationY Duan, L Wang, P A KollmanJournal of Molecular Graphics & Modelling|May 31, 2001
State of the art in studying protein folding and protein structure prediction using molecular dynamics methodsM R Lee, Y Duan, P A KollmanProteins|May 17, 2000
Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpieceM R Lee, Y Duan, P A KollmanJournal of Biomolecular Structure & Dynamics|December 1, 1994
Molecular dynamics simulations suggest that the Eco RI kink is an example of molecular strainS Kumar, Y Duan, P A Kollman, et al.Protein Science : a Publication of the Protein Society|July 1, 1999
Study of the stability and unfolding mechanism of BBA1 by molecular dynamics simulations at different temperaturesL Wang, Y Duan, R Shortle, et al.Proceedings of the National Academy of Sciences of the United States of America|December 10, 1999
Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7L T Chong, Y Duan, L Wang, et al.Journal of Computer-Aided Molecular Design|March 29, 2001
Does a diol cyclic urea inhibitor of HIV-1 protease bind tighter than its corresponding alcohol form? A study by free energy perturbation and continuum electrostatics calculationsL Wang, Y Duan, P Stouten, et al.Journal of Molecular Biology|October 31, 2000
Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent modelW Wang, P A KollmanProtein Engineering|February 1, 1991
Relative binding free energy calculations of inhibitors to two mutants (Glu46----Ala/Gln) of ribonuclease T1 using molecular dynamics/free energy perturbation approachesS Hirono, P A KollmanPageof 48