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alphafold2rave

alphageometry

alphamod

AlphaMod's official repository for protein folding

aqme

Automated Quantum Mechanical Environments (AQME) offers transparent and reproducible workflows available for Jupyter Notebooks and command lines, including: 1) RDKit- and CREST-based conformer generation, 2) QM input file creation, 3) post-processing of QM output files, 4) generation of xTB, DFT and RDKit descriptors. https://aqme.readthedocs.io

autodock4

aws-parallelcluster

AWS ParallelCluster is an AWS supported Open Source cluster management tool to deploy and manage HPC clusters in the AWS cloud.

bam_downloads

PGRR Download script for pulling data from CGHub

chemformer

cheminformatics

All the handy little scripts for cheminformatics related projects

chemprop

Message Passing Neural Networks for Molecule Property Prediction

datagrok-packages

Public package repository for the Datagrok.ai platform

datawarrior

Interactive data analysis and visualisation with chemical intelligence

descriptastorus

Descriptor computation(chemistry) and (optional) storage for machine learning

dimorphite_dl

Dimorphite-DL adds hydrogen atoms to molecular representations, as appropriate for a user-specified pH range. It is a fast, accurate, accessible, and modular open-source program for enumerating small-molecule ionization states.

distfit

distfit is a python library for probability density fitting.

effercio

Task Parallel Docking with Free Energy Correction

foldingdiff

Diffusion models of protein structure; trigonometry and attention are all you need!

geomol

gypsum_dl

Gypsum-DL is a free, open-source program that converts 1D and 2D small-molecule representations (SMILES strings or flat SDF files) into 3D models. It outputs models with alternate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational states.

janus

Python library for adaptive QM/MM methods

kartograf

This is an package contains tools for setting up hybrid-topology FE calculations

ketcher

Web-based molecule sketcher

lingo3dmol

math-lm

LLEMA

mdance

MDANCE is a flexible n-ary clustering package for all applications.

mmpdb

A package to identify matched molecular pairs and use them to predict property changes.

moler

Implementation of MoLeR: a generative model of molecular graphs which supports scaffold-constrained generation

molgpka

The graph-convolutional neural network for pka prediction

neuromancer

Pytorch-based framework for solving parametric constrained optimization problems, physics-informed system identification, and parametric model predictive control.

nglview

Jupyter widget to interactively view molecular structures and trajectories