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method-statistics

Here are 23 public repositories matching this topic...

Scindices / POVME--POVME3

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 / 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

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 / choderalab--pymbar

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 / KurtzmanLab--SSTMap

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 / biotite-dev--biotite

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 / choderalab--openmmtools

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 / cctbx--cctbx_project

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 / OpenFreeEnergy--openfe

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 / biopython--biopython

Official git repository for Biopython (originally converted from CVS)

status-active lang-python domain-bioinformatics 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 ecosystem-biopython

Updated Jul 28, 2026
Python

Scindices / markovmodel--PyEMMA

🚂 Python API for Emma's Markov Model Algorithms 🚂

lang-python status-archived entity-protein interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-machine-learning method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit

Updated Sep 11, 2023
Python

Scindices / msmbuilder--msmbuilder

🏗️ Statistical models for biomolecular dynamics 🏗️

lang-python status-archived entity-protein interface-api status-published status-packaged-conda scope-focused method-machine-learning method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory role-toolkit

Updated Jan 26, 2021
Python

Scindices / scverse--anndata

Annotated data.

status-active role-library lang-python domain-bioinformatics task-file-io interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-statistics task-system-model domain-single-cell entity-multi-omics ecosystem-scverse

Updated Jul 29, 2026
Python

Scindices / jensengroup--propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

status-active lang-python interface-cli role-application domain-structural-biology entity-protein interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics entity-complex method-statistics task-structure-prep task-charge-assignment domain-computational-chemistry

Updated Jul 14, 2026
Python

Scindices / Valdes-Tresanco-MS--gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

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

Updated Jul 27, 2026
Python

Scindices / scikit-bio--scikit-bio

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

status-active lang-python task-alignment domain-bioinformatics task-file-io 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 28, 2026
Python

Scindices / durrantlab--POVME

Detect and characterize binding pockets from molecular simulations.

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

Updated Mar 17, 2026
Python

Scindices / mooreneural--lacuna

Cryptic binding pocket discovery from conformational ensembles. Open-source, reproducible, size-robust benchmarks against fpocket, PocketMiner and CryptoBench.

status-active lang-python interface-cli role-application domain-structural-biology entity-protein interface-api scope-focused domain-drug-discovery task-pocket-detection method-machine-learning method-statistics domain-molecular-simulation task-trajectory-analysis entity-trajectory

Updated Jul 23, 2026
Python

Scindices / plinder-org--plinder

Protein Ligand INteraction Dataset and Evaluation Resource

status-active lang-python interface-cli domain-structural-biology entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-drug-discovery task-docking entity-complex method-statistics task-benchmark-dataset role-dataset

Updated Jul 25, 2026
Python

Scindices / mdtraj--mdtraj

An open library for the analysis of molecular dynamics trajectories

status-active lang-python lang-c task-file-io task-structure-analysis entity-protein entity-small-molecule 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 29, 2026
Python

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