DROIDS version 2.0 with much improved custom analyses is now released. Please go to https://github.com/gbabbitt/DROIDS-2.0---free-software-for-comparative-protein-dynamics
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.gitignore
1ubq.pdb
2ubq.pdb
2ubq_align.aln
Babbitt_etal2018_citation.pdf
Babbitt_etal2018_preprint.pdf
COPYING.txt
DROIDS 1.20 USER MANUAL.docx
DROIDS 1.20 USER MANUAL.pdf
DROIDS Installation Guide.rtf
DROIDS Installation Guide.txt
DROIDS_gstreamer.py
Descriptive.pm
GUI2_DROIDS.pl
GUI3_DROIDS.pl
GUI_SIMPLE_MD.pl
GUI_START_DROIDS.pl
GUI_START_DROIDS_dualGPU.pl
GranthamScores.txt
LICENSE
MD_protein.pl
MD_proteinQuery.pl
MD_proteinQuery_dualGPU.pl
MD_proteinReference.pl
MD_proteinReference_dualGPU.pl
QuickStartGuide.pdf
README.md
amino1to3.txt
color_by_attr_gray.py
color_by_attr_red.py
color_by_attr_tan.py
color_by_attr_yellow.py
render_movies_gray.py
render_movies_red.py
render_movies_tan.py
render_movies_yellow.py
teLeap_proteinQuery.pl
teLeap_proteinReference.pl

README.md

Our main goal is to try to visualize the impact of one of the longest time scale processes in the universe (i.e molecular evolution over 100s millions of years) on one of the shortest time scale processes (i.e. molecular motion over femtoseconds). To achieve this goal we use state-of-the-art biophysical simulations and graphics to design a gaming PC into a ‘computational microscope’ that is capable seeing how mutations and other molecular events like binding, bending and bonding affect the functioning of proteins and nucleic acids. DROIDS-1.0 (Detecting Relative Outlier Impacts in molecular Dynamic Simulation) is a GUI-based pipeline that works with AMBER16, Chimera 1.11 and CPPTRAJ to analyze and visualize comparative protein dynamics on GPU accelerated Linux graphics workstations. DROIDS employs a statistical method (multiple test corrected KS tests on all backbone atoms of each amino acid) to detect significant changes in molecular dynamics simulated on two homologous PDB structures. Quantitative differences in atom fluctuation are displayed graphically and mapped onto movie images of the protein dynamics at the level of individual residues. P values indicating significant changes are also able to be similarly mapped. DROIDS is useful for examining how mutations or binding interactions affect protein dynamics.DROIDS was produced by student effort at the Rochester Institute of Technology under the direction of Dr. Gregory A. Babbitt as a collaborative project between the Gosnell School of Life Sciences and the Biomedical Engineering Dept. Visit our lab website (https://people.rit.edu/gabsbi/) and download DROIDS 1.0 from Github at https://github.com/gbabbitt/DROIDS-1.0. We will be posting video results periodically on our youtube channel at https://www.youtube.com/channel/UCJTBqGq01pBCMDQikn566Kw