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Methods in Molecular Biology (Clifton, N.J.)|November 8, 2022
A Computational Framework for Determining the Breadth of Antibodies Against Highly Mutable PathogensSimone Conti, Martin KarplusPlos Computational Biology|April 11, 2019
Estimation of the breadth of CD4bs targeting HIV antibodies by molecular modeling and machine learningSimone Conti, Martin KarplusJournal of Computational Chemistry|August 5, 2022
ppdx: Automated modeling of protein-protein interaction descriptors for use with machine learningSimone Conti, Victor Ovchinnikov, Martin KarplusThe Journal of Chemical Physics|October 2, 2020
A restrained locally enhanced sampling method (RLES) for finding free energy minima in complex systemsVictor Ovchinnikov, Simone Conti, Martin KarplusJournal of Chemical Theory and Computation|February 12, 2020
Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell ModelVictor Ovchinnikov, Simone Conti, Edmond Y Lau, et al.Plos Computational Biology|April 20, 2022
Multiscale affinity maturation simulations to elicit broadly neutralizing antibodies against HIVSimone Conti, Victor Ovchinnikov, Jonathan G Faris, et al.Proceedings of the National Academy of Sciences of the United States of America|February 27, 2021
Design of immunogens to elicit broadly neutralizing antibodies against HIV targeting the CD4 binding siteSimone Conti, Kevin J Kaczorowski, Ge Song, et al.Biopolymers|February 26, 2003
Molecular dynamics of biological macromolecules: a brief history and perspectiveMartin KarplusAnnual Review of Biophysics and Biomolecular Structure|May 13, 2006
Spinach on the ceiling: a theoretical chemist's return to biologyMartin KarplusPageof 17