Speaker
Description
biochemical processes make the discovery of drugs and biomaterials possible. A research
framework common to genomics and proteomics is needed to conduct biomolecular
simulations that will connect biological data to the dynamic molecular mechanisms of
enzymes and proteins. Novice biomolecular modelers are faced with the daunting task of
complex setups and a myriad of possible choices preventing their use of molecular
simulations and their ability to conduct reliable and reproducible computations that can be
shared with collaborators and verified for procedural accuracy.
We present the foundations of BRIDGE 1 developed on the Galaxy platform 2 that makes
possible fundamental molecular dynamics and analysis of proteins through workflows and
pipelines via commonly used packages such as NAMD, GROMACS, CHARMM and
MDAnalysis. BRIDGE can be used to facilitate the set up and simulation of biological
macromolecules, perform conformational analysis from trajectory data and conduct data
analytics of large-scale protein motions using statistical rigor. All of these computational
tasks can be connected using workflows, for repeatability and automation, and then
distributed to run on cloud or HPC platforms. We illustrate the basic BRIDGE simulation
and analytics capabilities on a previously reported CBH1 protein simulation.
