Pinned Repositories
AF-cryptic-pocket
Cryptic pocket prediction using AlphaFold 2
BPTI-TICA-waterdynamics
tICA to capture local loop motion. Describes how to analyse loop movement using TICA and how to run PT-Metad using TIC vectors
Classifier-CV-sampling
Binary classifier as CV in enhanced sampling
Funnel-metadynamics
This repo is designed to give initial files to perform Funnel metadynamics as described in the paper Resolving the problem of trapped water in binding cavities: prediction of host–guest binding free energies in the SAMPL5 challenge by funnel metadynamics (https://link.springer.com/article/10.1007/s10822-016-9948-6)
Important-programmes
Histogram, bootstrapping and some analyses
Infrequent-metadynamics
Prediction of transition time (kinetics) associated with aromatic ring flipping using infrequent metadynamics
PAP-review-inputs
How one can use binary classifiers, variational auto-encoder, TICA, PCA, distance and dihedral order parameters as CVs in context of pepsin-like aspartic proteases e.g. BACE1 and plasmepsin-II.
Plasmepsin-bace
This repo provides all details to repertory and validate the paper Flap dynamics in pepsin-like aspartic proteases: a computational perspective using Plasmepsin-II and BACE-1 as model systems (doi: https://doi.org/10.1101/2020.04.27.062539)
Plotting-MD-Metadynamics
Jupyter Notebook showing how to plot FES, histograms and time-series data using Matplotlib.
sklearn-sfa
This project provides Slow Feature Analysis as a scikit-learn-style package.
sbhakat's Repositories
sbhakat/AF-cryptic-pocket
Cryptic pocket prediction using AlphaFold 2
sbhakat/Infrequent-metadynamics
Prediction of transition time (kinetics) associated with aromatic ring flipping using infrequent metadynamics
sbhakat/Classifier-CV-sampling
Binary classifier as CV in enhanced sampling
sbhakat/bayesian-flow-networks
This is the official code release for Bayesian Flow Networks.
sbhakat/colvar
A package that allows you to read COLVAR output from Plumed and access data
sbhakat/Important-programmes
Histogram, bootstrapping and some analyses
sbhakat/MSM-ring-flipping
Predicting kinetics of aromatic side-chain flipping using Markov State Model
sbhakat/alphaflow
AlphaFold Meets Flow Matching for Generating Protein Ensembles
sbhakat/aws-graviton-md-example
Helping MD customers run workloads on Graviton 3E instances (especially hpc7g) with optimized compiler settings
sbhakat/boltz
Official repository for the Boltz-1 biomolecular interaction model
sbhakat/CASTp-Plugin-for-PyMOL---Python3
CASTp Pocket Loader Plugin for PyMOL (Python 3 Update by me)
sbhakat/ClusterGCN
A PyTorch implementation of "Cluster-GCN: An Efficient Algorithm for Training Deep and Large Graph Convolutional Networks" (KDD 2019).
sbhakat/DiffDock
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
sbhakat/DiffusionProteinLigand
sbhakat/esmdiff
sbhakat/euporie
Jupyter notebooks in the terminal
sbhakat/frame-flow
Fast protein backbone generation with SE(3) flow matching.
sbhakat/gromacs-plumed-docker
sbhakat/gt4sd-core
GT4SD, an open-source library to accelerate hypothesis generation in the scientific discovery process.
sbhakat/Kinetics-from-AF
sbhakat/latex-nihbiosketch
A LaTeX class implementing the new NIH Biographical Sketch Format
sbhakat/md-sfa-msm
sbhakat/protein-interaction-network
Computes a molecular graph for protein structures.
sbhakat/ProteinCartography
a pipeline to build similarity maps of protein space
sbhakat/PyAutoFEP
PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
sbhakat/pygwalker
PyGWalker: Turn your pandas dataframe into a Tableau-style User Interface for visual analysis
sbhakat/rdkit
The official sources for the RDKit library
sbhakat/resume_coverletter_template
A resume+cover letter template made for Adobe InDesign/Illustrator
sbhakat/ufedmm
Unified Free Energy Dynamics (UFED) simulations with OpenMM
sbhakat/vidstream
Streaming video data via networks