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3d-rism-ai

ab_opt

Official implementation of Generative Diffusion Models for Antibody Design, Docking, and Optimization.

abs_dg_paper_chemscience2021

structures and data for https://doi.org/10.1039/D1SC03472C

af2complex

Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.

alphafold2-idr-complex-prediction

alphapulldown

amber-fb18

AMBER-FB18 phosphorylated amino acid force field parameters

awesome-cheminformatics

A curated list of Cheminformatics libraries and software.

awesome-cpp

A curated list of awesome C++ frameworks, libraries and software.

awesome-molecular-docking

We would like to maintain a list of resources which aim to solve molecular docking and other closely related tasks.

bat.py

The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems, compatible with the AMBER and OpenMM simulation packages.

bfee2

binding free energy estimator 2

comp.biochem.fun

An implementation of the SCF-DFT method with the focus on a reasonable balance between clear code and performance considerations.

crest

CREST - A program for the automated exploration of low-energy molecular chemical space.

cryo2struct

The programs for preprocessing cryo-EM density maps for machine learning

deepqm

dockq

DockQ is a single continuous quality measure for protein docked models based on the CAPRI evaluation protocol

fpocket

fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in

free-energy-landscape

geometry

Boost.Geometry - Generic Geometry Library

idp_lzerd

Modeling disordered protein interactions from biophysical principles

lmr-surfaceid

Repo contains source code of the SurfaceID paper

localcolabfold

ColabFold on your local PC

md_ligand_receptor

MD-ligand-receptor is a bioinformatics pipeline written in Python for analyzing non-covalent ligand-receptor interactions in 3D structures starting from a molecular dynamic trajectory.

minigpt-4

MiniGPT-4: Enhancing Vision-language Understanding with Advanced Large Language Models

mmseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

nonadditivityanalysis

Notebook for standardization of actvity data, nonadditivity analysis and its evaluation.

octree.didactic

An implementation of a *pseudo*-Octree with the focus on clear and comprehensible code. Intended to serve demonstrative and didactic purposes.

ommprotocol

A command line application to launch molecular dynamics simulations with OpenMM

openmm-atmmetaforce-plugin

An OpenMM plugin that implements the Alchemical Transfer Potential