Brief Research Description
Graduate Research Assistant, Levitt
Lab, Dept. of Structural Biology, Stanford University 09/2005-Present
- Accuracy of homology modeling
for structural genomics: Various potentials used to refine near-native
protein models to bring them closer to the actual structure using energy
minimization in vacuum and explicit water and molecular dynamics in
explicit and implicit solvent. [with C. Summa and M. Levitt]
- Stability of aromatic-rich
short peptide segments in hydrophobic collapse: Molecular Dynamics
in Gromacs with OPLS (10 ns) for each peptide rich in hydrophobic content
(high hydrophobic contacts and residues). Analysis of folding pathway
using hydrophobic-aided replica exchange. [with
X. Huang and M. Levitt]
- Structure of water around
non-polar solutes using first-principles: Using Quantum Mechanical
Polarizable Force Field run MD simulations (1ns) with benzene and cyclohexane. [with
M. Levitt]
- Alpha-helix denaturation
in a nano-droplet: Using molecular dynamics we ask: Can we do without
bulk solvent in protein folding? How does alpha-helix behave with a
shell of water around the protein? [with M. Levitt]
- Hybrid Knowledge based
potential for protein-protein docking: Developing a potential using
molecular mechanics, statistical and geometrical techniques for protein-protein
docking problems
[with J. Bernauer, K. Bastard and M. Levitt]
TEACHING EXPERIENCE
- SB228 Computaional Structural
Biology, Graduate Course, Stanford University (Fall 2006): Teaching
Assistant responsibilities included preparation and grading of course
assignments, updating online lectures and answering student questions
via email.
- Chem51 Organic Chemistry
Laboratory, Undergraduate Course, UC Irvine (Winter 2003): Instructor
responsibilities included directing the experiments in the laboratory,
grading the laboratory work and final exams.
PATENTS & PUBLICATIONS
- Chopra, G.; Summa, C.; Levitt
M., Atomic Potentials and Near-native Structure Refinement II: Implicit
and Explicit Models, paper in preparation.
- Chopra, G.; Levitt M.,
Structure of water around non-polar solutes using first principles:
Quantum Mechanical Polarizable Force-Field calculation,
paper in preparation.
- Chopra, G.; Levitt M.,
Protein Denaturation in a Nanodroplet,
paper in preparation.
- Chopra, G.; Anderson, S.,
Escutia, R., Self-Positioning Cardiac
Catheter System, U.S. provisional patent application Serial No.
60/556,533 (filed 3/25/2004).
- Chopra, G.; Gurushyam H.,
Generic Discrete Event Simulation Environment, Annual IT meet organized
by the Academic Interaction Council, Indian Institute of Technology,
New Delhi, Tryst, 2001 and on Mathematics Day conducted by the Mathematics
Society on 14th October 2001 in the celebration of the World
Mathematics, 2000.
LECTURE PRESENTATIONS
- Near-native Protein Structure
Refinement using Implicit and Explicit Models: Energy Minimization and
Molecular Dynamics, International Conference on Bioinformatics (InCoB),
New Delhi, India, 2006.
- Protein Denaturation in
a Nanodroplet, Stanford University Structural Biology Retreat, Asilomar,
CA, 2006.
POSTER PRESENTATIONS
- Chopra, G.; Levitt M.,
Stability of short aromatic-rich peptide segments in hydrophobic collapse,
International Conference on Bioinformatics, New Delhi, India, 2006;
Biomedical Computation at Stanford (BCATS), 2006 and BioX Symposium
at Stanford University, 2006.
- Chopra, G.; Levitt M.,
Protein Denaturation in a Nanodroplet,
Biomedical Computation at Stanford (BCATS), 2006.
WORKSHOPS
- Stanford Graduate Student
Institute (SGSI), Frontiers in Genetics: 8-day workshop in Genetics
(12-19 Sept. 2006), organized by Prof. Andrew Z. Fire and Prof. Richard
M. Myers.
