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method-rule-based

Here are 22 public repositories matching this topic...

Scindices / forlilab--Meeko

Interface for AutoDock, molecule parameterization

Updated Jul 10, 2026
Python

Scindices / PDBeurope--arpeggio

Calculation of interatomic interactions in molecular structures

role-library lang-python status-archived interface-cli domain-structural-biology entity-protein entity-small-molecule interface-api status-published status-packaged-pypi scope-focused domain-drug-discovery entity-complex method-rule-based task-interaction-analysis

Updated Sep 3, 2024
Python

Scindices / volkamerlab--teachopencadd

TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data

status-active lang-python interface-cli task-workflow role-application domain-structural-biology domain-cheminformatics entity-protein entity-small-molecule interface-jupyter status-published status-packaged-pypi status-packaged-conda domain-drug-discovery method-rule-based scope-suite

Updated Jul 23, 2026
Jupyter Notebook

Scindices / durrantlab--gypsum_dl

Open-source tool to generate 3D-ready small molecules for virtual screening

status-active lang-python interface-cli role-application domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi scope-focused domain-drug-discovery method-rule-based task-ligand-prep ecosystem-rdkit

Updated Nov 18, 2025
Python

Scindices / mcs07--MolVS

Molecule Validation and Standardization

role-library lang-python status-archived domain-cheminformatics task-file-io method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-rule-based task-ligand-prep ecosystem-rdkit

Updated Apr 16, 2020
Python

Scindices / BHM-Bob--fplip

Fast and All atom Protein-Ligand Interaction Profiler

status-active role-library lang-python interface-cli domain-structural-biology entity-protein entity-small-molecule interface-api status-packaged-pypi scope-focused domain-drug-discovery entity-complex task-trajectory-analysis entity-trajectory method-rule-based interface-gpu task-interaction-analysis

Updated Jul 27, 2026
Python

Scindices / Ensembl--ensembl-vep

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 / PDB-REDO--dssp

Application to assign secondary structure to proteins

status-active lang-python lang-cpp interface-cli role-application domain-structural-biology task-structure-analysis entity-protein interface-api status-published status-packaged-conda scope-focused method-rule-based

Updated Jun 23, 2026
C++

Scindices / rlabduke--MolProbity

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 / durrantlab--dimorphite_dl

Adds or removes hydrogen atoms to achieve the appropriate molecular protonation state for a user-specified pH range

status-active role-library lang-python interface-cli domain-cheminformatics method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-drug-discovery method-rule-based task-ligand-prep ecosystem-rdkit

Updated Dec 13, 2025
Python

Scindices / Valdes-Tresanco-MS--AutoDockTools_py3

Python3 translation of AutoDockTools

role-library lang-python status-archived interface-cli entity-protein entity-small-molecule interface-api scope-focused domain-drug-discovery task-docking entity-complex method-rule-based task-ligand-prep ecosystem-autodock

Updated May 31, 2024
Python

Scindices / chembl--ChEMBL_Structure_Pipeline

ChEMBL database structure pipelines

status-active role-library lang-python domain-cheminformatics task-file-io method-chemoinformatics entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-drug-discovery method-rule-based task-ligand-prep ecosystem-rdkit

Updated Nov 24, 2025
Python

Scindices / getcontacts--getcontacts

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation

status-active lang-python interface-cli role-application domain-structural-biology entity-protein status-published scope-focused entity-complex domain-molecular-simulation task-trajectory-analysis entity-trajectory method-rule-based task-interaction-analysis

Updated Jun 28, 2026
Python

Scindices / haddocking--pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

status-active lang-python 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 role-toolkit scope-swissknife entity-nucleic-acid task-structure-prep method-rule-based

Updated Jun 10, 2026
Python

Scindices / rlabduke--reduce

Reduce - tool for adding and correcting hydrogens in PDB files

status-active lang-cpp interface-cli role-application domain-structural-biology entity-protein status-published status-packaged-conda scope-focused method-physics entity-nucleic-acid task-structure-prep method-rule-based

Updated Jan 5, 2026
C++

Scindices / biotite-dev--hydride

Adding hydrogens to molecular models

status-active role-library lang-python interface-cli domain-structural-biology entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused method-physics task-structure-prep method-rule-based

Updated Nov 24, 2025
Python

Scindices / molinfo-vienna--apo2ph4

A versatile workflow for the generation of receptor-based pharmacophore models for virtual screening

status-active lang-python interface-cli task-workflow role-application domain-structural-biology method-chemoinformatics entity-protein entity-small-molecule status-published scope-focused domain-drug-discovery entity-complex method-rule-based task-pharmacophore

Updated May 22, 2025
Python

Scindices / openmm--pdbfixer

PDBFixer fixes problems in PDB files

status-active role-library lang-python interface-cli domain-structural-biology task-file-io entity-protein interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-molecular-simulation task-structure-prep method-rule-based interface-gui ecosystem-openmm

Updated Mar 10, 2026
Python

Scindices / pharmai--plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake, Bolz, et al. (2025), https://doi.org/10.1093/nar/gkaf361

status-active lang-python interface-cli role-application domain-structural-biology entity-protein entity-small-molecule interface-api status-published status-packaged-pypi status-packaged-conda scope-focused domain-drug-discovery entity-complex method-rule-based task-interaction-analysis

Updated Jul 3, 2026
Python

Scindices / dwhswenson--contact_map

Contact map analysis for biomolecules; based on MDTraj

status-active role-library lang-python domain-structural-biology entity-protein interface-api status-published status-packaged-pypi status-packaged-conda scope-focused entity-complex domain-molecular-simulation task-trajectory-analysis entity-trajectory method-rule-based task-interaction-analysis

Updated May 9, 2026
Python

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