hSMD code, scripts, and coordinates for protein-protein affinity

Published: 11-11-2018| Version 2 | DOI: 10.17632/tghr5d9zgx.2
Contributor:
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Description

This data has three parts: 1. C++ code for hSMD. 2. NAMD2.13 with hSMD binary on a linux workstation with cuda. 3. All the parameters, coordinates, structures, and scripts to reproduce the results of this paper: Computing Protein-Protein Association Affinity with Hybrid Steered Molecular Dynamics. Rodriguez RA, Yu L, Chen LY. Journal of chemical theory and computation. 2015; 11(9):4427-4438. NIHMSID: NIHMS719598 PubMed [journal]PMID: 26366131 PMCID: PMC4565455

Files

Steps to reproduce

1. tar zxvf *.gz 2. go to rasral/100-equil and the MD simulations in the bound state 3. go to rasral and run hSMD pullings 4. go 200-apo and run the MD simulations in the dissociated state