Stanford University
Chemistry
Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations have been used to determine the electronic structures of two Mo bis-dithiolene complexes, [Mo(OSi)(bdt)2]1− and [MoO(OSi)(bdt)2]1−, where... more
The similarities and differences in the fundamental coordination chemistry of molybdenum and tungsten mainly in physiological oxidation states MIV–VI are examined in relation to the properties of enzyme sites that catalyze oxygen atom... more
Improved rational drug design methods are needed to lower the cost and increase the success rate of drug discovery and development. Alchemical binding free energy calculations, one potential tool for rational design, have progressed... more
- by Vijay Pande
By employing thousands of PCs and new worldwide-distributed computing techniques, we have simulated in atomistic detail the folding of a fast-folding 36-residue α-helical protein from the villin headpiece. The total simulated time exceeds... more
- by Vijay Pande
Summary Unused CPU time on desktop computers could be put to good use, if distributed computing succeeds in capturing people's imagination. In their Perspective, Shirts and Pande describe existing distributed computing projects and recent... more
- by Vijay Pande
Recent hardware and software advances have enabled simulation studies of protein systems on biophysically relevant time scales, often revealing the need for improved force fields. Although early force field development was limited by the... more
- by Vijay Pande
Theoretical studies using simplified models of proteins have shed light on the general heteropolymeric aspects of the folding problem. Recent work has emphasized the statistical aspects of folding pathways. In particular, progress has... more
- by Vijay Pande
Abstract. Despite their immense importance to cellular function, the precise mechanism by which chaperonins aid in the folding of other proteins remains unknown. Experimental evidence seems to imply that there is some diversity in how... more
- by Vijay Pande
Abstract: When accounting for structural fluctuations or measurement errors, a single rigid structure may not be sufficient to represent a protein. One approach to solve this problem is to represent the possible conformations as a... more
- by Vijay Pande
Abstract We suggest a procedure to synthesize polymers with characteristics similar to those observed in globular proteins: renaturability and the existence of an" active site" capable of specifically recognizing a given target molecule.... more
- by Vijay Pande
Understanding the mechanism of protein folding is a notori-ously difficult problem for both experiment and simulation (1, 2). In this issue of PNAS, through a combination of theory (Karanicolas and Brooks; ref. 3) and experiment (Nyguen... more
- by Vijay Pande
Abstract There are many unresolved questions regarding the role of water in protein folding. Does water merely induce hydrophobic forces, or does the discrete nature of water play a structural role in folding? Are the nonadditive aspects... more
- by Vijay Pande
Abstract Implementation of molecular dynamics (MD) calculations on novel architectures will vastly increase its power to calculate the physical properties of complex systems. Herein, we detail algorithmic advances developed to accelerate... more
- by Vijay Pande
The folding of proteins in confined spaces is a ubiquitous theme in biological and biomaterial applications, including folding in chaperones1 and pores, 2 nanotube-based drug delivery, 3 and cotranslational folding of nascent peptides in... more
- by Vijay Pande
LINGOs are a holographic measure of chemical similarity based on text comparison of SMILES strings. We present a new algorithm for calculating LINGO similarities amenable to parallelization on SIMD architectures (such as GPUs and vector... more
- by Vijay Pande
▪ Abstract Simulation of protein folding has come a long way in five years. Notably, new quantitative comparisons with experiments for small, rapidly folding proteins have become possible. As the only way to validate simulation... more
- by Vijay Pande