Vedasheersh

CatPred

Machine Learning models for in vitro enzyme kinetic parameter prediction

Protein-InDelMaker

A Rosetta-based Python tool for constructing user-defined variant libraries with amino acid insertions, deletions, using loop closure algorithms and energy minimization.

acsbiot

autodock_pipeline

(semi) Automatic pipeline for autodock vina docking

baker_scripts

xmls,pyrosetta,etc.

biopandas

Working with molecular structures in pandas DataFrames

Flex_Index_IDP

Calculate flexibility index for an Intrinsically Disordered Protein from MD trajectories

PISA_parser

Parse protein interface data from the PDBe PISA server

PyRosetta_routines

Routines or scripts written in PyRosetta

schrodinger-md-automation

scripts to automate schrodinger simulations

Vedasheersh/biopandas

Working with molecular structures in pandas DataFrames

Vedasheersh/brenda-parser

Python codes to parse the full Brenda database text file

Vedasheersh/Flex_Index_IDP

Calculate flexibility index for an Intrinsically Disordered Protein from MD trajectories

Vedasheersh/schrodinger-md-automation

scripts to automate schrodinger simulations

Vedasheersh/chemprop

Message Passing Neural Networks for Molecule Property Prediction

Vedasheersh/Computational_Mutational_Scan_Rosetta

Vedasheersh/ConPLex

Adapting protein language models and contrastive learning for highly-accurate drug-target interaction prediction.

Vedasheersh/ddG_sars

Vedasheersh/DeepConv-DTI

DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences

Vedasheersh/DeepFRI

Deep functional residue identification

Vedasheersh/DiffDock

Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

Vedasheersh/DLKcat

Deep learning and Bayesian approach applied to enzyme turnover number for the improvement of enzyme-constrained genome-scale metabolic models (ecGEMs) reconstruction

Vedasheersh/Enzyme-Promiscuity-Prediction

Vedasheersh/EnzymePromiscuityClassification

Vedasheersh/InterMol

Conversion tool for molecular simulations

Vedasheersh/kcat_km_prediction

Vedasheersh/kcat_prediction

Vedasheersh/KM_prediction

Vedasheersh/molgraph

Graph neural networks for molecular machine learning. Implemented and compatible with TensorFlow and Keras.

Vedasheersh/nn4dms

Neural networks for deep mutational scanning data

Vedasheersh/protease-gcnn-pytorch

Vedasheersh/Protein-InDelMaker

PyRosetta based package to make PDB files for specified mutations, insertions and deletions

Vedasheersh/protein_bert

Vedasheersh/PSG-BAR

This is the code for our paper Ligand Binding Prediction using Protein Structure Graphs and Residual Graph Attention Networks

Vedasheersh/SARSr-CoV_homolog_survey

Survey of ACE2 binding specificities among SARS-related CoV homologs

Vedasheersh/ScanNet

Vedasheersh/streamlit-example

Example Streamlit app that you can fork to test out share.streamlit.io

Vedasheersh/tf-bind-transformer

A repository with exploration into using transformers to predict DNA ↔ transcription factor binding

Vedasheersh/ThioesteraseEnzymeSpecificity

Vedasheersh/vedasheersh.github.io