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Scindices / choderalab--perses

Experiments with expanded ensembles to explore chemical space

status-active lang-python interface-cli role-framework entity-protein entity-small-molecule interface-api status-published status-packaged-conda scope-focused domain-drug-discovery method-physics entity-complex method-statistics domain-molecular-simulation ecosystem-openmm task-free-energy

Updated Oct 28, 2025
Python

Scindices / prody--ProDy

Star

A Python Package for Protein Dynamics Analysis

status-active lang-python domain-structural-biology task-file-io task-structure-analysis entity-protein interface-api status-published status-packaged-pypi status-packaged-conda method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit scope-swissknife

Updated Jul 22, 2026
Python

Scindices / POVME--POVME3

Star

A pocket volume analyzer for use in protein modeling.

lang-python status-archived interface-cli role-application domain-structural-biology entity-protein interface-api status-published status-packaged-pypi scope-focused domain-drug-discovery task-pocket-detection method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory

Updated Oct 2, 2022
Python

Scindices / rlabduke--MolProbity

Star

Protein and nucleic acid validation service

interface-web lang-perl status-archived interface-cli role-application domain-structural-biology task-structure-analysis entity-protein status-published scope-focused method-statistics entity-nucleic-acid method-rule-based

Updated Mar 7, 2024
Perl

Scindices / arq5x--bedtools2

Star

bedtools - the swiss army knife for genome arithmetic

status-active lang-cpp lang-c domain-bioinformatics interface-cli role-application task-file-io status-published status-packaged-conda scope-focused method-statistics entity-nucleic-acid task-sequence-analysis entity-sequence domain-genomics

Updated Jun 10, 2026
C

Scindices / KurtzmanLab--SSTMap

Star

Solvation Structure and Thermodynamic Mapping

status-active lang-python lang-cpp interface-cli role-application entity-protein interface-api status-published scope-focused domain-drug-discovery method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory task-free-energy

Updated Dec 17, 2025
Python

Scindices / project-gemmi--gemmi

Star

macromolecular crystallography library and utilities

status-active lang-python lang-cpp interface-cli domain-structural-biology task-file-io task-structure-analysis method-chemoinformatics entity-protein interface-api status-published status-packaged-pypi status-packaged-conda method-statistics role-toolkit scope-swissknife task-structure-prep entity-crystal domain-crystallography

Updated Jul 24, 2026
C++

Scindices / iqtree--iqtree2

Star

IQ-TREE software version 2: phylogenetics by maximum likelihood

status-active lang-cpp domain-bioinformatics interface-cli role-application entity-protein status-published status-packaged-conda scope-focused method-statistics entity-nucleic-acid task-sequence-analysis entity-sequence

Updated Jul 22, 2026
C++

Scindices / choderalab--pymbar

Star

Python implementation of the multistate Bennett acceptance ratio (MBAR)

status-active role-library lang-python interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-statistics domain-molecular-simulation entity-trajectory task-free-energy

Updated Feb 12, 2026
Python

Scindices / cctbx--cctbx_project

Star

Computational Crystallography Toolbox

status-active lang-python lang-cpp interface-cli domain-structural-biology task-file-io task-structure-analysis entity-protein interface-api status-published status-packaged-conda method-physics method-statistics role-toolkit scope-swissknife task-structure-prep entity-crystal domain-crystallography

Updated Jul 29, 2026
Python

Scindices / Amber-MD--pytraj

Star

Python interface of cpptraj

status-active role-library lang-python lang-cpp task-file-io entity-protein interface-api status-published status-packaged-conda scope-focused method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory

Updated Mar 6, 2026
Jupyter Notebook

Scindices / OpenFreeEnergy--openfe

Star

The Open Free Energy toolkit

status-active lang-python interface-cli role-framework entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda domain-drug-discovery method-physics entity-complex method-statistics domain-molecular-simulation scope-suite ecosystem-openmm task-free-energy ecosystem-openfe

Updated Jul 29, 2026
Python

Scindices / wolberlab--dynophores

Star

Dynamic pharmacophore modeling of molecular interactions

role-library lang-python status-archived method-chemoinformatics entity-protein entity-small-molecule interface-api interface-jupyter status-published status-packaged-conda domain-drug-discovery entity-complex method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory scope-swissknife task-pharmacophore task-interaction-analysis

Updated Apr 26, 2024
Promela

Scindices / KrumkachevaLab--EPR-BindingSite

Star

Identification of Protein-Ligand Binding Sites using dipolar EPR data

status-active lang-python interface-cli role-application domain-structural-biology entity-protein entity-small-molecule status-published scope-focused domain-drug-discovery task-binding-site method-physics entity-complex method-statistics

Updated Apr 12, 2025
Jupyter Notebook

Scindices / glotzerlab--freud

Star

Powerful, efficient particle trajectory analysis in scientific Python.

status-active role-library lang-python lang-cpp task-structure-analysis interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory entity-crystal domain-materials

Updated Jul 29, 2026
C++

Scindices / choderalab--openmmtools

Star

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

status-active role-library lang-python entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics method-statistics domain-molecular-simulation entity-trajectory ecosystem-openmm task-md-engine task-free-energy

Updated Jan 7, 2026
Python

Scindices / Amber-MD--cpptraj

Star

Biomolecular simulation trajectory/data analysis.

status-active lang-cpp interface-cli task-file-io task-structure-analysis entity-protein entity-small-molecule interface-api status-published method-physics method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit scope-swissknife

Updated Jul 16, 2026
C++

Scindices / biotite-dev--biotite

Star

A comprehensive library for computational molecular biology

status-active lang-python domain-bioinformatics domain-structural-biology task-file-io task-structure-analysis method-chemoinformatics entity-protein interface-api status-published status-packaged-pypi status-packaged-conda method-statistics role-toolkit scope-swissknife entity-nucleic-acid task-sequence-analysis entity-sequence

Updated Jul 21, 2026
Python

Scindices / Ensembl--ensembl-vep

Star

The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

status-active lang-python lang-perl domain-bioinformatics interface-cli role-application status-published status-packaged-conda scope-focused method-statistics entity-nucleic-acid entity-sequence method-rule-based domain-genomics task-variant-analysis

Updated Jul 24, 2026
Perl

Scindices / DerrickWood--kraken2

Star

The second version of the Kraken taxonomic sequence classification system

status-active lang-python lang-cpp domain-bioinformatics interface-cli role-application status-published status-packaged-conda scope-focused method-statistics entity-nucleic-acid task-sequence-analysis entity-sequence domain-genomics

Updated Jul 29, 2026
C++

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method-statistics

Here are 41 public repositories matching this topic...

Scindices / choderalab--perses

Scindices / prody--ProDy

Scindices / POVME--POVME3

Scindices / rlabduke--MolProbity

Scindices / arq5x--bedtools2

Scindices / KurtzmanLab--SSTMap

Scindices / project-gemmi--gemmi

Scindices / iqtree--iqtree2

Scindices / choderalab--pymbar

Scindices / cctbx--cctbx_project

Scindices / Amber-MD--pytraj

Scindices / OpenFreeEnergy--openfe

Scindices / wolberlab--dynophores

Scindices / KrumkachevaLab--EPR-BindingSite

Scindices / glotzerlab--freud

Scindices / choderalab--openmmtools

Scindices / Amber-MD--cpptraj

Scindices / biotite-dev--biotite

Scindices / Ensembl--ensembl-vep

Scindices / DerrickWood--kraken2

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