DROIDS 4.0 + maxDemon 2.0
Linux software pipeline for machine learning assisted MD ensemble analysis for comparative protein dynamics
DOWNLOAD .tar.gz DOWNLOAD .zip AMBER INSTALLER .zip DROIDS INSTALLER .zipUser Manual
A descriptive general user manual for concept, implementation advice and troubleshooting
Link to PDF
The G.A.Babbitt Lab at the Rochester Institute of Technology
Our research
Our research is focused upon gaining a better understanding of how the biophysical function of proteins, DNA and other molecules constrains molecular evolution. We employ a computational approach, taking advantage of many methods in computer simulation, machine learning, statistics and traditional bioinformatics. We are working closely Dr. Ernest Fokoue's research group to develop machine learning applications to molecular dynamics.
Our group
Our research group consists of primarily undergraduate students working in many programs across RIT, including Biomedical Engineering, Biotechnology, Biology, Computer Science, Math and Bioinformatics. Most students work for the lab on a volunteer basis, with very flexible schedules, working towards publishable projects that can be added to a students' resume.
How to join our group?
Students interested in working with the lab should contact me at gabsbi(at)rit.edu. Volunteers should have some proficiency in either computer programming, mathematics and/or molecular biology and be willing to commit about a year of their spare time towards the goals of the group.
Our lab YouTube channel
Here we post interesting project results, movies and educational tutorials
YouTubeMore about me
PubMed listing my CV Am Sci 2011 cover story masters thesis Univ FL 2000 PhD dissertation Univ FL 2006 my first publication 1991Courses I teach
I currently teach Cell and Molecular Biology for Engineers I and II, Bioinformatics Languages, Statistics for Bioinformatics, Introduction to Bioinformatics, and Computational Methods in Statistics and Data Science (graduate). I have periodically taught courses in Molecular Evolution and Biomimicry as well.
If you publish your results...
To cite DROIDS and maxDemon, please see the links below
first citation - Biophysical Journal second citation - Biophysical Journal third citation - STAR Protocolspublished examples from our lab
Function and evolution of B-Raf loop dynamics relevant to cancer recurrence under drug inhibition, Journal of Biomolecular Structure and Dynamics, DOI: 10.1080/07391102.2020.1815578
Online Link PDFFunctional binding dynamics relevant to the evolution of zoonotic spillovers in endemic and emergent Betacoronavirus strains. , Journal of Biomolecular Structure and Dynamics, DOI: 10.1080/07391102.2021.1953604
Online Link PDFOperating System Requirements
DROIDS is tested upon Linux Mint 18/19 with Amber 16/18 and OpenMM. Amber only runs on Linux. Any Debian desktop OS (e.g. Ubuntu) should work. We prefer Linux Mint because its Driver Manager greatly eases the management of Nvidia graphics drivers during initial system build. See also our instructions for running Virtual Machines on Windows and Google Cloud.
Graphics Processor Requirements
Nvidia GTX 1080, RTX 2080 or Titan X are recommended. DROIDS can utilize systems with single GPU, dual independent GPUs, or multiple GPUs connected by SLI. NOTE: Amber requires additional testing on SLI stacks. Nvidia GPU enabled Ubuntu Linux Virtual Machines instances are very easy to build on the Google Cloud Platform.
Licensing
DROIDS+maxDemon is freely distributed under GPL3 license. GPU accelerated Amber 18 is licensed under Univ of CA. See the Amber homepage for purchase details (https://ambermd.org/). Alternatively, the open source OpenMM python library can be used.
Major Software Dependencies
Nvidia CUDA 9.0 and CUDA Dev tools, MD software = Amber16/18(licensed) or OpenMM (open source), R software, UCSF Chimera software for molecular visualization.
Installation
We supply a flexible installer script (perl DROIDS+AMBERinstaller.pl) with the main tar.gz file. It will install DROIDS, CUDA, Ambertools, OpenMM and all other dependencies. Also see instructions in the DROIDS installation file, tutorial and user manual.