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3d-af_surfer

aa-score-tool

a tool for protein-ligand binding affinity prediction

aaproperties

aaProperties takes in one or two multiple sequence alignments as input, “cleans” the data into a suitable format and then converts it to a sequence of properties. Depending on if the user used one or two alignments as input, he or she can now either compare the two amino acid sequences against each other, compare the two property sequences against each other, compare individual amino acid sequences against their respective properties or write one of the pairs (amino acid plus properties) into a comma separated file.

ai-bind

Interpretable AI pipeline improving binding predictions for novel protein targets and ligands

alchemical-setup

alchemlyb

the simple alchemistry library

amazon-sagemaker-examples

Example 📓 Jupyter notebooks that demonstrate how to build, train, and deploy machine learning models using 🧠 Amazon SageMaker.

amdock

(Linux) AMDock: Assisted molecular docking with AutoDock4 and AutoDockVina

aminoacidplotting

Uses protein file codes to download the corresponding mmCif file from PDB and plot the number of each amino acid in the file

autodock-gpu

AutoDock for GPUs and other accelerators

autodock-vina

AutoDock Vina

autodocktools_py3

Python3 translation of AutoDockTools

bat.py

The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems.

binding_site_fitter

Python / C++ GUI application for fitting binding site data

bindingsitesfromfragments

De novo design of small molecule binding sites into proteins

bio-yodie

Bio-YODIE is GATE's biomedical named entity linking pipeline.

bionoinet

BionoiNet is a deep learning-based software to classify ligand-binding sites.

bitenet

Spatiotemporal identification of druggable binding sites using deep learning

blues

Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling

blues-flexible-ligand

contains files for blues-flexible-ligand paper

catalytic-triad-detection

Detect catalytic triads in serine protease PDB files based on geometry

chemformer

clinicaltrialsparser

Python classes / functions to parse Clinical Trial data in the form of XML returned from clinicaltrials.gov. Older version also allows for parsing of Json returned from Lilly COI API.

clustal-omega

Multiple sequence aligner for protein and DNA/RNA.

colabfold

Making Protein folding accessible to all via Google Colab!

combind

Integrated physics-based and ligand-based modeling.

d4m.jl

A D4M module for Julia. D4M was developed in MATLAB by Dr Jeremy Kepner.

d4m.py

A D4M module for Python. D4M was developed in MATLAB by Dr Jeremy Kepner

datamol

Molecular Manipulation Made Easy.

dedupe

:id: A python library for accurate and scalable fuzzy matching, record deduplication and entity-resolution.