Our research lab develops and optimizes biomolecular simulation methods (molecular dynamics, replica-exchange, and free energy methods) and force fields mainly in the context of the AMBER package. Recent successes include very accurate structure modeling of DNA duplexes, spontaneous ligand binding to multiple nucleic acid targets, and the spontaneous observation of low population Hoogsteen base pairing in poly d(AT) duplexes. Recently the lab has also been investigating "staples" (i.e. adding ligands that bridge two separated atoms in a molecule to try to increase stability) both in the context of i to i+4 and i to i+7 linkages in proteins, and various P-P, and O-O linkages in nucleic acids (with all the associated stereochemistries where relevant). The lab has also begun investigates of the use of the Drude polarizable force fields for nucleic acids and various H-REMD schemes for force field validation, assessment and improvement.

Recent successes in the simulation of unbiased or spontaneous processes in proteins and nucleic acids

Fall 2022 abstracts, posters, and presentations will launch in mid-September.

ACS Fall 2022

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.