Dataset Open Access

Barnase-Barstar Binding Pathways

Ali S. Saglam; Lillian T. Chong; Page O. Harrison

This is a collection of binding trajectories from the atomistic simulation of the Barnase-Barstar system presented in Protein–protein binding pathways and calculations of rate constants using fully-continuous, explicit-solvent simulations by Saglam and Chong. There is one representative trajectory from each of the five pathways identified.

The GRO file here is to be used as a "topology" file, so if your chosen MD viewer or analysis software includes the reference frame from the GRO file, be sure to delete the frame before running your analysis, etc. If you want to analyze just the first frame of a trajectory, load in the GRO/topology file, delete the frame from that file, load in the relevant XTC file and use the first frame from that.

Please cite the Saglam and Chong paper if you use these data.

This work was supported by NSF CAREER Award MCB-0845216 and NIH 1R01GM115805-01 to LT Chong and a DAAD graduate research grant to AS Saglam. Computational resources were provided by NSF XSEDE allocation TG-MCB100109 to LT Chong, NSF CNS-1229064, and the University of Pittsburgh's Center for Research Computing.
Files (2.8 GB)
Name Size
bound_paths.tar.gz
md5:a7c186dfc7f2c5de0434eab58f055063
1.4 GB Download
trackI.xtc
md5:932656b60e454d3d948399c527c1fa50
207.2 MB Download
trackI_imaged.xtc
md5:488cfbd35589e7927d598622f3644b94
206.5 MB Download
trackI_topology.gro
md5:b79b7cd60a0ebfe4b728861ccf7f8974
151.8 kB Download
trackII.xtc
md5:644305ff71ca76792d60eb2c5771fb91
108.7 MB Download
trackII_imaged.xtc
md5:7fd537003cbafb1c08bfa9c3bc927582
108.4 MB Download
trackII_topology.gro
md5:1e094062f091598715c105ade52bffc0
151.8 kB Download
trackIII.xtc
md5:40c2c7cb42b0c42030191bb45bfcbb38
153.7 MB Download
trackIII_imaged.xtc
md5:2c845a1b02501e3009cc614c421a1326
153.6 MB Download
trackIII_topology.gro
md5:50cc87a6f0de9c2d4f60f15b9aabf691
151.8 kB Download
trackIV.xtc
md5:32224aa5b8336e895849a2369267ee97
206.5 MB Download
trackIV_imaged.xtc
md5:32224aa5b8336e895849a2369267ee97
206.5 MB Download
trackIV_topology.gro
md5:e2ce6068e886d25882acabbc35020632
151.8 kB Download
trackV.xtc
md5:83608ea3c735f47b18ae0f1805d6e06a
42.6 MB Download
trackV_imaged.xtc
md5:83608ea3c735f47b18ae0f1805d6e06a
42.6 MB Download
trackV_topology.gro
md5:1405c74f5ddcc8da3a55d2dd55ef9cdf
151.8 kB Download
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