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University of California, San Francisco


UCSF's innovative, collaborative approaches for patient care, research and education span disciplines across the life sciences and make it a world leader in scientific discovery and its translation into improved health.




  • Canonical protein-protein interface 100 ns trajectories. ( Software )

    The project contains GROMACS trajectories of protein-protein complexes in explicit water. The trajectories are compressed XTC files. Trajectory details: 1) 10 x 10ns GROMACS trajectories sampled every 10ps 2) equilibrated 200ps under NVT then 1ns under NPT, production runs under NPT ensemble 3) OPLSAA parameters 4) SPC water Protein-protein complex details: 1) Barnase-Barstar 2) Immunoglobulin-Antigen 3) Trypsin-Trypsin Inhibitor 4) TEM-BLIP Information about how to download the trajectories is in the wiki.

  • Climber: a non-linear protein trajectory morphing method ( Software )

    We present a new morphing method that does not move linearly and can therefore go around high energy barriers, and which can produce different trajectories between the same two starting points. The input are two protein conformations (an initial and final conformation) and an alignment that will define which inter-residue distances are restrained to reach the final structure.

  • Simulation of Coronary Artery Bypass Graft and Surgical Ventricular Restoration ( Software )

    This project is a virtual surgery tool for enabling clinicians to easily simulate the effects of coronary artery bypass graft (CABG) and surgical ventricular restoration (SVR) on patients with ischemic heart failure.

    Keywords: CABG, finite element, SVR

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Last updated: 2013-10-01T12:17:15.492-04:00

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