Pinned Repositories
alchemical-analysis
An open tool implementing some recommended practices for analyzing alchemical free energy calculations
alchemical-analysis-feedstock
A conda-smithy repository for alchemical-analysis.
alchemical-best-practices
Best practice document for alchemical free energy calculations going to livecoms journal
alchemlyb
the simple alchemistry library
AlGDock
Molecular docking with Alchemical Interaction Grids
apbs-pdb2pqr
Fork of PDB2PQR including HTMD & py36 fixups (use htmd-fixups branch)
awesome-materials-informatics
Curated list of known efforts in materials informatics
awesome-molecular-generation
Awesome papers related to generative molecular modeling and design.
awesome-python-chemistry
A curated list of Python packages related to chemistry
tsenapathi's Repositories
tsenapathi/awesome-molecular-generation
Awesome papers related to generative molecular modeling and design.
tsenapathi/awesome-python-chemistry
A curated list of Python packages related to chemistry
tsenapathi/BFEE2
binding free energy estimator 2
tsenapathi/BioGPT
tsenapathi/chemprop
Message Passing Neural Networks for Molecule Property Prediction
tsenapathi/deepFMPOv3D
Implementation of Shape and Electrostatic similarity metric in deepFMPO.
tsenapathi/Ensembler
tsenapathi/espsim
Scoring of shape and ESP similarity with RDKit
tsenapathi/exmol
Explainer for black box models that predict molecule properties
tsenapathi/FEgrow
An Open-Source Molecular Builder and Free Energy Preparation Workflow
tsenapathi/gmx_MMPBSA
gmx_MMPBSA is a new tool aid to perform end-state free energy calculations based on AMBER's MMPBSA.py with GROMACS files.
tsenapathi/Jupyter_Dock
Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.
tsenapathi/md-davis
MD DaVis: A python package to analyze molecular dynamics trajectories of proteins
tsenapathi/mdfptools
tsenapathi/NeuralPLexer
NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
tsenapathi/openmm-tutorial-msbs
OpenMM tutorial for the MSBS course
tsenapathi/openmm_sdm_workflow
Example of the use of the single-decoupling method setup workflow
tsenapathi/pdb2pqr-feedstock
A conda-smithy repository for pdb2pqr.
tsenapathi/Pocket2Mol
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets
tsenapathi/poltype2
Poltype 2: Automated Parameterization and Free Energy Prediction for AMOEBA
tsenapathi/PyAutoFEP
PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
tsenapathi/pyCHARMM-Workshop
pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the University of Michigan by Charles Brooks' Group, June 20-24.
tsenapathi/qmmm-workshop
Workshop teaching QMMM using Amber
tsenapathi/rdkit
The official sources for the RDKit library
tsenapathi/reeds
This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration free energies or ligand binding free energies.
tsenapathi/ScaffoldGraph
ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees.
tsenapathi/soapgp
Molecular Property Prediction using GP with a SOAP kernel
tsenapathi/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
tsenapathi/tsenapathi.github.io
tsenapathi/wepy
Weighted Ensemble simulation framework in Python