Pande Lab

We use computer simulation, statistical mechanics, and Bayesian statistics to tackle challenging problems in chemical biology, biophysics, and biomedicine.

Projects

We work on a range of projects, with the collective goal of pushing the limits of computational and theoretical methods and applying them to important problems in biophysics and biophysical chemistry.

Theoretical Chemistry

We are breaking fundamental barriers in molecular simulation by developing new paradigms for supercomputing through worldwide distributed computing and Graphics Processing Units (GPUs); long timescale kinetics, including MD simulations of millisecond events in all atom detail; and sampling algorithms for more precise free energy calculation. Learn more.

Biophysical Chemistry

Feynman famously stated in his 1963 Lectures, “Everything that living things do can be understood in terms of the jiggling and wiggling of atoms.” Modern biophysics, however, has only begun to connect the microscopic motions and forces of atoms to biological function. Our lab aims to bridge this gap using atomic molecular simulation to study protein dynamics, both folding and conformational change. Learn more.

Biomedical Applications

Drug discovery is very expensive and time-consuming and only a tiny fraction of drug candidates ever receives approval for human use. Our lab develops new methods for virtual screening and molecular similarity calculations. We then apply chemical similarity methods to identify therapeutics for disease, with ongoing projects involving Malaria, Chagas disease, and Dengue fever. Learn more.

People

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Directed by Dr. Vijay Pande, the award-winning team at Stanford University’s Pande Lab has been responsible for several advances in the fields of theoretical biophysical chemistry.  Our lab has a diverse group of people, with backgrounds including physical science (physics, chemistry), statistics, computer science, biology, and biomedicine. Current Group … Learn More

Software

One hallmark of our lab is the development of novel, open source software to push the limits of molecular simulation methods and to bring these capabilities to the field in general. Some key examples are shown below, with more on our Software page.

Folding@home

Folding@home is a distributed computing project -- people from throughout the world download and run software to band together to the largest supercomputer in the world. Folding@home uses novel computational methods coupled to distributed computing, to simulate problems millions of times more challenging than previously achieved. Learn more.

MSM Builder

Understanding a molecule’s conformational dynamics requires mapping out the dominant metastable, or long lived, states that it occupies and then determining the rates for transitioning between these states. Markov State Models (MSMs) provide a natural framework for accomplishing this objective. To facilitate more widespread use of MSMs we have developed the MSMBuilder package. Learn more.

OpenMM

OpenMM is a library which provides tools for modern molecular modeling simulation. As a library it can be hooked into any code, allowing that code to do molecular modeling with minimal extra coding. Moreover, OpenMM has a strong emphasis on hardware acceleration, thus providing not just a consistent API, but much greater performance than what one could get from just about any other code available. Learn more.

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