SergeiNikolenko/LPCE

The LPCE project is designed to purify and process PDB structures to extract and filter ligands and remove unwanted components such as water molecules and junk ligands.

Language: Jupyter Notebook - Size: 13.6 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 1 - Forks: 0

BioPandas/biopandas

Working with molecular structures in pandas DataFrames

Language: Python - Size: 22.3 MB - Last synced at: 2 days ago - Pushed at: 9 months ago - Stars: 727 - Forks: 120

project-gemmi/gemmi

macromolecular crystallography library and utilities

Language: C++ - Size: 9.92 MB - Last synced at: 2 days ago - Pushed at: 9 days ago - Stars: 256 - Forks: 47

horsicq/PDBRipper

PDBRipper is a utility for extract an information from PDB-files.

Language: C - Size: 1.76 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 828 - Forks: 90

biotite-dev/biotite

A comprehensive library for computational molecular biology

Language: Python - Size: 180 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 785 - Forks: 110

microsoft/SQLCallStackResolver

A sample tool for users of Microsoft SQL Server to aid in troubleshooting otherwise difficult to diagnose issues. Provided AS-IS - see SUPPORT.md.

Language: C# - Size: 11.8 MB - Last synced at: 4 days ago - Pushed at: 13 days ago - Stars: 47 - Forks: 14

mdtraj/mdtraj

An open library for the analysis of molecular dynamics trajectories

Language: Python - Size: 34.5 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 633 - Forks: 288

PDB-REDO/libcifpp

Library containing code to manipulate mmCIF and PDB files

Language: C++ - Size: 11.3 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 35 - Forks: 14

HoShiMin/formatPE

A bunch of parsers for PE and PDB formats in C++

Language: C++ - Size: 81.1 KB - Last synced at: 17 days ago - Pushed at: 11 months ago - Stars: 237 - Forks: 49

SergiR1996/PELEAnalysis-Processing

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

Language: Python - Size: 51.1 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 1 - Forks: 2

moritzobenauer/ProjectRaccoon

Automated construction of atomistic and coarse-grained models in the PDB format for polymer peptide conjugates.

Language: Jupyter Notebook - Size: 8.37 MB - Last synced at: 2 days ago - Pushed at: 10 months ago - Stars: 6 - Forks: 1

Biswa96/PDBDownloader

Standalone program to download PDB Symbol files for debugging without WDK

Language: C - Size: 28.3 KB - Last synced at: 19 days ago - Pushed at: almost 6 years ago - Stars: 75 - Forks: 25

molstar/VSCoding-Sequence

VSCode Extension for interactively visualising protein structure data in the editor

Language: TypeScript - Size: 99.5 MB - Last synced at: 18 days ago - Pushed at: 5 months ago - Stars: 104 - Forks: 10

project-gemmi/pdb-stats

Clickable PDB statistics: synchrotrons and MX software

Language: JavaScript - Size: 7.68 MB - Last synced at: 11 days ago - Pushed at: about 2 months ago - Stars: 8 - Forks: 4

ISDementyev/pmUE

pmUE (Protein Modelling Unreal Engine) - a repo for constructing a molecule visualizer plugin in Unreal

Language: C++ - Size: 37.2 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 6 - Forks: 3

normcyr/new-pdb-inspector 📦

Search for new PDB structures corresponding to a search term and deposited after a certain date.

Language: Python - Size: 19.5 KB - Last synced at: 15 days ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 0

IBCHgenomic/proteogenomics

proteogenomics for protein analysis

Language: Rust - Size: 6.58 MB - Last synced at: 27 days ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

a-r-j/CPDB

Cython implementation of PDB -> DataFrame parsing

Language: Cython - Size: 18.7 MB - Last synced at: 18 days ago - Pushed at: almost 2 years ago - Stars: 23 - Forks: 0

shred/commons-pdb 📦

Read PalmOS PDB files with Java

Language: Java - Size: 39.1 KB - Last synced at: 3 days ago - Pushed at: 2 months ago - Stars: 5 - Forks: 1

Sarah-Hesham-2022/Unity-Protein-Visualization

Protein Visualization using Unity and C# analysis on PDB Files.

Language: C# - Size: 229 KB - Last synced at: 5 days ago - Pushed at: about 2 years ago - Stars: 14 - Forks: 1

project-gemmi/wasm

Parts of Gemmi in WebAssembly.

Language: HTML - Size: 5.76 MB - Last synced at: 11 days ago - Pushed at: 3 months ago - Stars: 3 - Forks: 1

fantin-mesny/amapec

Antimicrobial activity prediction for fungal effector candidates

Language: Python - Size: 19.2 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

smx-smx/PDBSharp

Fast and cross-platform parser for Microsoft PDB files

Language: C# - Size: 731 KB - Last synced at: 10 days ago - Pushed at: 6 months ago - Stars: 33 - Forks: 4

darwinsorchid/Frataxin-Structure-Analysis

[Python] Structural bioinformatics analysis of the human frataxin protein involved in Friedreich's Ataxia (FRDA).

Language: Python - Size: 31.3 KB - Last synced at: 19 days ago - Pushed at: 6 months ago - Stars: 1 - Forks: 0

jgreener64/pdb-benchmarks

Benchmarking common tasks on proteins in various languages and packages

Language: Python - Size: 1.93 MB - Last synced at: 13 days ago - Pushed at: over 4 years ago - Stars: 41 - Forks: 6

pswanson1/PPM

PPM.Mk.I.Beta

Language: Python - Size: 58.6 KB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0

SeanCline/PythonSymbols

A WinDbg symbol server for all recent versions of CPython.

Language: Python - Size: 2.46 GB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 24 - Forks: 0

haschka/pdb2fasta

Extracts the fasta sequence from protein stored in a PDB file

Language: C - Size: 26.4 KB - Last synced at: 2 months ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

haschka/pdb-nma-analysis

A tool to perform quick normal mode analysis on a PDB file using Tirion's model.

Language: C - Size: 27.3 KB - Last synced at: 2 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

gromacstutorials/.github

GROMACS tutorials for both beginners and advanced users

Size: 15.6 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

gu1729/pdbdump

Dump content of PDB files (program databases) in JSON, XML, SQLite3, CSV etc.

Language: C++ - Size: 317 KB - Last synced at: 9 months ago - Pushed at: over 3 years ago - Stars: 35 - Forks: 8

Warpv/allatom-polymere-system-in-VMD

create allatom polymere system from .xyz file in VMD

Size: 32.2 KB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

OmerRaviv/PdbBenchmarks

Benchmark for the most popular managed PDB readers.

Language: C# - Size: 1.09 MB - Last synced at: 25 days ago - Pushed at: about 3 years ago - Stars: 6 - Forks: 0

johnnytam100/pdb2uniprot

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

Language: Python - Size: 15.6 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 8 - Forks: 0

PombertLab/3DFI

The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space.

Language: Perl - Size: 110 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 16 - Forks: 7

Sarah-Hesham-2022/BioPhysics-Molecular-Dynamics-Simulation

Using VMD and NAMD for molecular dynamics simulation of protein PDB files.

Language: Tcl - Size: 57.3 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 2

mindleaving/genome-tools

Tools for exploration and analysis of biochemical data like genomics and proteins

Language: C# - Size: 905 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 4 - Forks: 2

bhagesh-codebeast/Bioinformatics

Language: Jupyter Notebook - Size: 1000 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

Spenhouet/PDBViewer

Visualization of proteins directly from the PDB database or from a .pdb file.

Language: Java - Size: 7.19 MB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 3 - Forks: 3

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 .

Language: Python - Size: 47.9 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 11 - Forks: 4

matheuspokkkk/ppdistance

defines the interface region of a protein complex making possible to calculate the i_rmsd between native and predicted structures following the CAPRI criteria

Language: C - Size: 42 KB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 2 - Forks: 0

gkoulouras/PDB-amino-acid-ratio

A console application for the ration calculation of amino acids from a PDB file.

Language: Visual Basic - Size: 531 KB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

hocinebib/PisaPy

Python code to automatically interact with PDBePISA web server

Language: Python - Size: 48.8 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 5 - Forks: 1

fovtran/nvc19_repo

ncovpub

Language: Jupyter Notebook - Size: 54.8 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

JMB-Scripts/CIF-to-PDB

Convert in batch CIF files to PDB

Language: Python - Size: 5.86 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

metaworm/pdb-viewer

PDB Viewer powered by Rust + WASM, high performance, no backend. https://pdbview.metaworm.site/ http://pdb.metaworm.site/

Language: HTML - Size: 761 KB - Last synced at: about 2 months ago - Pushed at: almost 2 years ago - Stars: 8 - Forks: 0

continuous-symmetry-measure/pdb_prep

PDB file parser and prepare tools.

Language: Python - Size: 4.38 MB - Last synced at: over 1 year ago - Pushed at: about 3 years ago - Stars: 3 - Forks: 3

mmagnus/emacs-pdb-mode

pdb-mode is an emacs-lisp minor mode for Emacs to perform a number of useful editing functions on Protein DataBank (PDB) formatted files. XEmacs and/or GNU Emacs are available for most computing platforms.

Language: Emacs Lisp - Size: 351 KB - Last synced at: 12 months ago - Pushed at: over 2 years ago - Stars: 13 - Forks: 6

Sarah-Hesham-2022/TCL-TK-VMD-PDB

TCL-TK for VMD.

Language: Tcl - Size: 230 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 0

Broihon/Symbol-Parser

Small class to parse debug info from PEs, download their respective PDBs from the Microsoft Public Symbol Server and calculate RVAs of functions

Language: C++ - Size: 35.2 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 21 - Forks: 11

jewettaij/dlpdb

collect statistics from the entire PDB library

Language: Python - Size: 2.02 MB - Last synced at: 9 days ago - Pushed at: about 3 years ago - Stars: 5 - Forks: 4

gkoulouras/seq-sec-ratio

A console application for the estimation of the primary and secondary structure's elements. Input should be the FASTA-formatted "ss.txt" file generated by PDB database.

Language: Visual Basic - Size: 812 KB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 3 - Forks: 0

HebaFahmy99/Bioinformatics-Project

A Tcl program starts with displaying a menu for the user to choose a specific action and based on his/her action start to call the appropriate answer.

Language: Tcl - Size: 208 KB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

mmp1100000/pyRosetta

pyRosseta Workshop

Language: Jupyter Notebook - Size: 15.6 KB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 2 - Forks: 1

continuous-symmetry-measure/pdbslicer

Bisect protein file (PDB) into sub units (i.e amino acids)

Language: Perl - Size: 2.3 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

aalhossary/CrossLinX

CrossLinX is the acronym of protein CrossLINks eXplorer.

Language: Java - Size: 105 MB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

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

Language: Python - Size: 4.88 KB - Last synced at: almost 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

AJVelezRueda/Be_project

Bioinformatics pipeline for parsing PED data

Language: Python - Size: 3.98 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

ignatovmg/NRGmin

Utility for molecular mechanics energy minimization with OpenMP support

Language: Rich Text Format - Size: 1.79 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

ignatovmg/mol_grid

Small library for conversion of pdb files into numpy grids

Language: Python - Size: 908 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 1

Krnds/ProjetPDB

Java command line tool for fetching, parsing and displaying in a Jmol window all interactions zones between proteins or molecular complexes

Language: Java - Size: 14.3 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

hocinebib/3D_Visual_pdb_py

3D vizualisation of pdb files with python

Language: Python - Size: 643 KB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

ning-y/jPdbApi

A Java wrapper for the RCSB PDB REST APIs

Language: Java - Size: 19.5 KB - Last synced at: about 2 months ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

shivChitinous/rad-gyres

calculating radii of gyration of proteins from .pdb files

Language: Jupyter Notebook - Size: 42.6 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

AndreaRubbi/pdb_parser

Python program that can identify the residues interacting between chains of a complex protein.

Language: Python - Size: 14.6 KB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

babinyurii/PyRAMA Fork of gerdos/PyRAMA

Python implementation of the Ramachandran plot

Language: Jupyter Notebook - Size: 1.33 MB - Last synced at: about 2 years ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

julianspaeth/pdb-viewer

A PDB Viewer Application implemented completely in JavaFX

Language: Java - Size: 31.3 KB - Last synced at: about 2 years ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

CorbanSwain/QChem-PDB-Corrector

Python script to correct misformated x, y, and z coordinates output by Q Chem simulations.

Language: Python - Size: 4.88 KB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

obliviateandsurrender/PDB-Reader

This script aims at reading a given PDB file and generation dihedral angles from it.

Language: Python - Size: 73.2 KB - Last synced at: 6 months ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

obliviateandsurrender/ORF-finder-Protien-Sequence-Generator

This script allows us to generate ORF for a given Protein Sequence.

Language: Python - Size: 7.81 KB - Last synced at: 6 months ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0