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Current Opinion in Structural Biology|August 30, 2021
How much can physics do for protein design?Eleni Michael, Thomas SimonsonProtein Science : a Publication of the Protein Society|March 19, 2024
Classifying protein kinase conformations with machine learningIvan Reveguk, Thomas SimonsonProteins|June 15, 2026
Physics-Based Energy Functions for Computational Protein DesignThomas GaillardThe Journal of Physical Chemistry. B|October 7, 2025
Improved Physics-Based Single-Position Protein Sequence Redesign with a Residue-Pairwise Generalized Born ModelThomas GaillardJournal of Chemical Information and Modeling|July 11, 2018
Evaluation of AutoDock and AutoDock Vina on the CASF-2013 BenchmarkThomas GaillardChembiochem : a European Journal of Chemical Biology|January 13, 2006
Free-energy simulations and experiments reveal long-range electrostatic interactions and substrate-assisted specificity in an aminoacyl-tRNA synthetaseDamien Thompson, Pierre Plateau, Thomas SimonsonScientific Reports|November 22, 2017
Computational design of fully overlapping coding schemes for protein pairs and tripletsVaitea Opuu, Martin Silvert, Thomas SimonsonAccounts of Chemical Research|June 19, 2002
Free energy simulations come of age: protein-ligand recognitionThomas Simonson, Georgios Archontis, Martin KarplusMethods in Molecular Biology (Clifton, N.J.)|March 17, 2022
Knowledge-Based Unfolded State Model for Protein DesignVaitea Opuu, David Mignon, Thomas SimonsonJournal of Molecular Recognition : JMR|August 21, 2009
Alchemical free energy simulations for biological complexes: powerful but temperamentalAlexey Aleksandrov, Damien Thompson, Thomas SimonsonPageof 16