Research Interests

Computational Chemistry / Biophysical Chemistry

The research in my lab focuses on the development and application of computational chemistry techniques to solve interesting problems that exist at the interface of chemistry, biology, and medicine. I currently have three main areas of interest:

1. Examination of structure, dynamics, and mechanism. Specifically, this focuses on two main areas; examination of antibiotic and inhibitor resistance mechanisms with hybrid quantum mechanical and molecular mechanical (QM/MM) methods and elucidation of carbohydrate structure and dynamics as related to energy production. This includes the development of new simulation and analysis techniques with a primarily focuses on multi-scale modeling methods, techniques for computing free energies of enzymatically catalyzed reactions, and methods for probing the normal modes of complex systems.

2. Development and application of computer aided drug design techniques. I am interested in applying my expertise in protein structure-function to the development of novel inhibitors targeted towards problems ranging from cancer to antibiotic design. Additionally, I would like to extend current drug design strategies to take advantage of more advanced techniques from computational chemistry (i.e. QM/MM, normal mode analysis, etc.).

3. Application of computational chemistry to understand bio-organic, organic, and organo-metallic chemistry. Specifically, I am interested in exploring structure and stability as they relate to the detailed physical orbital picture. This is an essential part of understanding the physical world and gives experimental scientists the insight they need to explore new chemistry.

Thursday, July 03, 2008


  • is a versatile and widely used molecular simulation program with broad application to many-particle systems
  • has been developed with a primary focus on the study of molecules of biological interest, including peptides, proteins, prosthetic groups, small molecule ligands, nucleic acids, lipids, and carbohydrates, as they occur in solution, crystals, and membrane environments
  • provides a large suite of computational tools that encompass numerous conformational and path sampling methods, free energy estimates, molecular minimization, dynamics, and analysis techniques, and model-building capabilities
  • is useful for a much broader class of many-particle systems
  • can be utilized with various energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potentials with explicit solvent and various boundary conditions, to implicit solvent and membrane models
  • has been ported to numerous platforms in both serial and parallel architectures




CHARMMing contains an integrated set of tools for uploading structures, performing simulations, and viewing the results. In order to provide the best possible user experience, it incorporates a number of freely available tools such as Jmol for visualization and an automatic residue topology file (RTF) generator (GENRTF) which generates the necessary information for atoms and residues that are currently not supported by the CHARMM force fields. Below is a partial list of functionality that currently is incorporated into CHARMMing.org:

  • A CHARMM tutorial that has been specifically designed for novice CHARMM users
  • PDB/CRD reader and input script generator
  • Integrated molecular graphics
  • Integrated simulation tools (i.e. minimization, solvation, dynamics)
  • Automatic topology generation

CHARMMing was developed by the Laboratory of Computational Biology. Planning and development were done by:

* Rishi Singh
* Tim Miller
* Jeff Klauda
* Milan Hodoscek (GENRTF)
* H. Lee Woodcock *

With special thanks to:

* Bernard Brooks
* Rick Venable
* Xiongwu Wu



CHARMM Tutorial
Rishi P. Singh, Benjamin T. Miller, Jeffery Klauda, Xiongwu Wu, and H. Lee Woodcock


A tutorial/introduction to the use of CHARMM has been created and published on the web (CHARMM Tutorial). In addition, this has been integrated into CHARMMing. This tutorial provides conceptual foundations to molecular simulation techniques such as energy minimization, solvation, molecular dynamics, and the use of periodic boundary conditions that are implemented in CHARMMing. Thus CHARMMing may be used as an introduction to molecular simulations in general and CHARMM in particular with the tutorial serving as a manual.

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