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pdb-files

Here are 31 public repositories matching this topic...

mdtraj / mdtraj

An open library for the analysis of molecular dynamics trajectories

python pdb molecular-dynamics dihedral-angles mdtraj rmsd pdb-files molecular-dynamics-trajectories

Updated Nov 4, 2025
Python

biotite

biotite-dev / biotite

A comprehensive library for computational molecular biology

bioinformatics structural-biology computational-biology pdb-files sequence-analysis

Updated Oct 30, 2025
Python

BioPandas / biopandas

Working with molecular structures in pandas DataFrames

bioinformatics pdb molecular-structures pandas-dataframe protein-structure molecule computational-biology drug-discovery molecules mol2 pdb-files

Updated Aug 1, 2024
Python

jgreener64 / pdb-benchmarks

Benchmarking common tasks on proteins in various languages and packages

bioinformatics pdb comparison benchmarks mmcif structural-bioinformatics mmtf pdb-files

Updated Dec 27, 2020
Python

lucagl / MOAD_ligandFinder

A script able to extract ligands from pdb structure(s) and remove them from the original structure. The ligands are identified according to the *valid* ligands found in the binding MOAD database. The ligand can be extracted as a pdb or as a xyz (coordinate) file. Other options such as converting the queried pdb to pqr are available .

pdb-files ligands pqr-files binding-moad extract-ligand remove-ligands

Updated Jul 13, 2022
Python

hocinebib / PisaPy

Python code to automatically interact with PDBePISA web server

csv interface xml protein-structure protein xml-parser pdb-files

Updated Jun 27, 2022
Python

jewettaij / dlpdb

collect statistics from the entire PDB library

structural-bioinformatics pdb-files

Updated Feb 18, 2022
Python

continuous-symmetry-measure / pdb_prep

PDB file parser and prepare tools.

chemistry proteins python3 pdb-files rscb

Updated Feb 23, 2022
Python

JMB-Scripts / CIF-to-PDB

Convert in batch CIF files to PDB

pdb cif mmcif pdb-files

Updated Oct 27, 2023
Python

johnnytam100 / pdb2uniprot

A Python script to map PDB ID + chain ID to UniProt ID.

bioinformatics mapping uniprot uniprot-ids bioinformatics-scripts uniprotkb pdb-files pdb-database bioinformatics-tool rcsb pdb-structure

Updated Mar 7, 2024
Python

SergiR1996 / PELEAnalysis-Processing

This repository contains Python scripts to analyze MD & PELE simulations, to preprocess & process the system (pdb files), and many more.

pdb-files pele-simulation md-simulation

Updated Apr 2, 2025
Python

hocinebib / 3D_Visual_pdb_py

3D vizualisation of pdb files with python

python structure mayavi pdb-files 3d-vizualisation

Updated Oct 3, 2020
Python

SeanCline / PythonSymbols

A WinDbg symbol server for all recent versions of CPython.

python pdb windbg pdb-files

Updated Jul 18, 2025
Python

ignatovmg / mol_grid

Small library for conversion of pdb files into numpy grids

grid pdb cnn pdb-files

Updated Oct 19, 2021
Python

fantin-mesny / amapec

Antimicrobial activity prediction for fungal effector candidates

machine-learning annotation proteins structures prediction fungi effector antimicrobial-peptides pdb-files antimicrobial

Updated Jul 31, 2025
Python

bjaan / dll-exports-ordinal-name-ghidra-script

This Python script for Ghidra will export a table of function names and corresponding ordinals of a DLL, when other tools fail to do so

reverse-engineering exports size-coding dynamic-link-library pdb-files ghidra-scripts

Updated Jan 7, 2022
Python

helykopter8484 / Ion_Environments_Project

pdb biopython subprocess pdb-files ion-environments

Updated Mar 12, 2018
Python

hkabbech / DSSP_implt

Programming project (Python) - Implementation of the DSSP method (Secondary Structure Assignment)

dssp python3-6 pdb-files

Updated Sep 20, 2018
Python

pswanson1 / PPM

PPM.Mk.I.Beta

protein-structure python3 pdb-files protein-database ubiquitination-site ubiquitinylation

Updated Aug 15, 2024
Python

mlund / pdb2xyz

Convert PDB files to coarse grained XYZ files

protein-structure coarse-graining pdb-files molecular-modeling

Updated Jul 2, 2025
Python

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