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gromacswrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2023 supported).

hbind

Calculates hydrogen-bond interaction tables for protein-small molecule complexes, based on protein PDB and protonated ligand MOL2 structure input. Raschka, Wolf, et al. (2018) J. Computer-Aided Molec. Design

hbindviz

Generates a script to visualize protein-ligand H-bonds from an Hbind interaction table (see separate Hbind module) for display by PyMOL. Raschka, Wolf et al. (2018) J. Computer-Aided Molec. Design

hgnc-gene-family-mapper

Draws a map of a HGNC gene family hierarchy for a family

hicolm3

Multi-Methods for Molecules and Condensed Systems

homep3.1

htmd

HTMD: Programming Environment for Molecular Discovery

ideogram

Chromosome visualization for the web

igv.js

Embeddable genomic visualization component based on the Integrative Genomics Viewer

ihag

Interactive horizontal acyclic grapher

im-docs

Documentation for the InterMine project

in-depth-ngs-data-analysis-course

interactiondrawer

InteractionDrawer is a JavaScript library for the drawing of highly interactive 2D ligand interaction diagrams.

intermine

A powerful open source data warehouse system

intermol

Conversion tool for molecular simulations

inverse-molecular-design

Autonomous generator of novel organic compounds from target physicochemical properties. It accelerates innovations in novel materials and/or drugs with specific target properties.

jannovar

Annotation of VCF variants with functional impact and from databases (executable+library)

jax-md

Differentiable, Hardware Accelerated, Molecular Dynamics

jbrowse

JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.

jupyter_dock

Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.

jvarkit

Java utilities for Bioinformatics

langchain

⚡ Building applications with LLMs through composability ⚡

largecsv2mysql

a php script to import very large csv file to Mysql database

learn_cryoem_math

lightaimd

A lightweight ab initio molecular dynamics simulation program

ligpargen

Command line tool providing BOSS generated OPLS-AA/CM1A(-LBCC) parameters for organic molecules and ligands.

ligpargentools

Scripts to set up condensed phase simulations using of LigParGen Server

ligro

lincs-workshop-2020

CMap Notebooks for LINCS 2020 Workshop

litmatter

Rapid experimentation and scaling of deep learning models on molecular and crystal graphs.