Gilson Group Info Page:R&D

Research & Development
Gilson Laboratory

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Overview

Our work focuses on the application of theory, computer models, and informatics to noncovalent binding and molecular recognition. We are particularly interested in developing software and data resources that will be of value in understanding these phenomena and in designing molecules that bind to specific targets.

Research Areas

Updated April, 2012

Changes in protein and ligand entropy as determinants of affinity; preorganization and entropy-enthalpy compensation
Calculation of configurational entropy from molecular dynamics simulations
Development of mathematical approaches to computation of entropy
Role of water structure and thermodynamics in molecular recognition and drug design
Modeling water by explicit simulation and continuum models
Theory and method for calculation of binding free energies: double decoupling, pulling, etc.
Computational analysis of mechanical stress at the molecule level
Role of stress in molecular mechanisms, such as allostery and DNA bending
Modeling host-guest systems and supramolecular systems
Host-guest systems as models of protein-ligand binding and test cases for modeling techniques
Force field development
Mechanisms and dynamics of protein kinases, especially protein kinase A
Computer-aided drug-design in collaboration with experimental groups
Design of drugs for malaria
Computational studies of natural products and their interactions with proteins
BindingDB: a publicly accessible database of measured protein-small molecule affinities