microResearcher's Projects
AnnapuRNA: a scoring function for predicting RNA-small molecule interactions.
AutoDock Vina
Calculation of Biomolecular Dimensions for AutoDock VINA Docking and Other Operations
Source code for molecular graphics program UCSF ChimeraX
Dr. Basu Lab Student Code
Python functions for simulating mathematical models, estimating model parameters, quantifying uncertainties and visualizing results.
Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
Create force-directed graphs of RNA secondary structures.
Conversion tool for molecular simulations
API for Unsub
NAMD simulation setup for a an example setup of polypeptide
Plotting graphs from XVGs generated by GROMACS in Python
inferring sequence-structure motifs using deep learning
Animation engine for explanatory math videos
MDAnalysis is a Python library to analyze molecular dynamics simulations.
microcontroller
Code Contributor
OpenMM is a toolkit for molecular simulation using high performance GPU code.
PDBFixer fixes problems in PDB files
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to š Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
An automated drug discovery pipeline
Python utility lib for easy file and data handling