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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.
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.
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