pdb-files

There are 3 repositories under pdb-files topic.

PDBRipper
horsicq / PDBRipper
PDBRipper is a utility for extract an information from PDB-files.
pdb-files pdb-parser pdb reverse-engineering hacktoberfest hacktoberfest2023
Language:C 790
BioPandas / biopandas
Working with molecular structures in pandas DataFrames
molecular-structures pandas-dataframe pdb mol2 protein-structure molecules pdb-files drug-discovery computational-biology bioinformatics molecule
Language:Python 708
biotite
biotite-dev / biotite
A comprehensive library for computational molecular biology
bioinformatics computational-biology structural-biology sequence-analysis pdb-files
Language:Python 613
mdtraj / mdtraj
An open library for the analysis of molecular dynamics trajectories
molecular-dynamics python mdtraj rmsd dihedral-angles pdb pdb-files molecular-dynamics-trajectories
Language:Python 584
HoShiMin / formatPE
A bunch of parsers for PE and PDB formats in C++
cpp header-only modern-cpp pdb pdb-files pdb-parser pdb-structure pe pe-analyzer pe-applications pe-file pe-format pe-parser portable-executable
Language:C++ 220
project-gemmi / gemmi
macromolecular crystallography library and utilities
cif mmcif crystallography protein-structure molecular-structures ccp4 pdb-files structural-biology mtz
Language:C++ 217
molstar / VSCoding-Sequence
VSCode Extension for interactively visualising protein structure data in the editor
vscode vscode-extension protein protein-structure pdb pdb-files molstar molecule structural-biology structure
Language:TypeScript 96
Biswa96 / PDBDownloader
Standalone program to download PDB Symbol files for debugging without WDK
pdb pdb-files pdb-database windows c reverse-engineering reversing
Language:C 71
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.
sqlserver sqlserver-2017 sqlserver-2022 azuresql azuresqldb azuresqlmanagedinstance callstack debugging msdia140 pdb pdb-files sqlserver-2019 debugging-symbol sre symbols tool xevent xevents
Language:C# 42
jgreener64 / pdb-benchmarks
Benchmarking common tasks on proteins in various languages and packages
pdb pdb-files benchmarks comparison bioinformatics structural-bioinformatics mmcif mmtf
Language:Python 41
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
pdb-files
Language:C++ 39
gu1729 / pdbdump
Dump content of PDB files (program databases) in JSON, XML, SQLite3, CSV etc.
code code-quality developer-tools pdb pdb-database pdb-files windows
Language:C++ 36
smx-smx / PDBSharp
Fast and cross-platform parser for Microsoft PDB files
csharp debug debug-symbols library microsoft microsoft-pdb parser pdb-files pdb-parser
Language:C# 30
PDB-REDO / libcifpp
Library containing code to manipulate mmCIF and PDB files
mmcif pdb-files protein-structure
Language:C++ 28
SeanCline / PythonSymbols
A WinDbg symbol server for all recent versions of CPython.
pdb pdb-files python windbg
Language:Python 24
a-r-j / CPDB
Cython implementation of PDB -> DataFrame parsing
bioinformatics deep-learning machine-learning pdb pdb-files pdb-parser protein protein-structure structural-biology
Language:Cython 19
PombertLab / 3DFI
The 3DFI pipeline predicts the 3D structure of proteins and searches for structural homology in the 3D space.
3d-structure pdb-files structural-homologs
Language:Perl 17
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
Language:Python 14
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.
pdb-files pdb rna-structure-prediction rna-structure rna-pdb
Language:Emacs Lisp 14
johnnytam100 / pdb2uniprot
A Python script to map PDB ID + chain ID to UniProt ID.
bioinformatics bioinformatics-scripts bioinformatics-tool mapping pdb-database pdb-files pdb-structure rcsb uniprot uniprot-ids uniprotkb
Language:Python 13
Sarah-Hesham-2022 / Unity-Protein-Visualization
Protein Visualization using Unity and C# analysis on PDB Files.
bioinformatics csharp file-analysis pdb-files problem-solving protein-structure structural-bioinformatics structural-biology unity visualization
Language:C# 11
hocinebib / PisaPy
Python code to automatically interact with PDBePISA web server
protein protein-structure interface xml xml-parser csv pdb-files
Language:Python 9
metaworm / pdb-viewer
PDB Viewer powered by Rust + WASM, high performance, no backend. https://pdbview.metaworm.site/ http://pdb.metaworm.site/
pdb pdb-files reverse-engineering
Language:HTML 8
project-gemmi / pdb-stats
Clickable PDB statistics: synchrotrons and MX software
protein-data-bank statistics x-ray-crystallography cross-filter pdb-files synchrotron
Language:JavaScript 7
ISDementyev / pmUE
pmUE (Protein Modelling Unreal Engine) - a repo for constructing a molecule visualizer plugin in Unreal
cpp pdb pdb-files virtual-reality protein-structure protein-modeling protein-sequence protein unreal-engine molecular-modeling molecule-viewer molecule-visualization molecules
Language:C++ 6
OmerRaviv / PdbBenchmarks
Benchmark for the most popular managed PDB readers.
pdb-files pdb-parser portable-pdb windows-pdb
Language:C# 6
Sarah-Hesham-2022 / BioPhysics-Molecular-Dynamics-Simulation
Using VMD and NAMD for molecular dynamics simulation of protein PDB files.
bioinformatics biophysics force-filed molecular-dynamics-simulation namd nanoscale-molecular-dynamics pdb-files problem-solving programming proteins structural-bioinformatics structural-biology tcl-tk trajectory visualization-molecular-dynamics visulaization vmd waterbox
Language:Tcl 6
jewettaij / dlpdb
collect statistics from the entire PDB library
pdb-files structural-bioinformatics
Language:Python 5
mindleaving / genome-tools
Tools for exploration and analysis of biochemical data like genomics and proteins
genomics genomic-data-analysis genomics-visualization molecular-dynamics molecular-structures molecule peptide molecular-simulation pdb pdb-files
Language:C# 5
ProjectRaccoon
moritzobenauer / ProjectRaccoon
Automated construction of atomistic and coarse-grained models in the PDB format for polymer peptide conjugates.
cheminformatics molecular-dynamics-simulation molecular-modeling pdb-files
Language:Jupyter Notebook 5
shred / commons-pdb
Read PalmOS PDB files with Java
java palmos pdb-files library
Language:Java 5
continuous-symmetry-measure / pdb_prep
PDB file parser and prepare tools.
pdb-files chemistry python3 proteins rscb
Language:Python 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.
pdb pdb-files ss-txt amino-acids secondary-structure bioinformatics-data bioinformatics-scripts bioinformatics-databases vb-net protein-data-bank protein-sequences protein-secondary-structure bioinformatics
Language:Visual Basic 3
project-gemmi / wasm
Parts of Gemmi in WebAssembly.
mmcif pdb-files wasm
Language:HTML 3
Spenhouet / PDBViewer
Visualization of proteins directly from the PDB database or from a .pdb file.
3d-viewer pdb pdb-database pdb-files protein protein-data-bank
Language:Java 3
Sarah-Hesham-2022 / TCL-TK-VMD-PDB
TCL-TK for VMD.
bioinformatics pdb-files problem-solving protein protein-structure scripting structural-bioinformatics structural-biology tcl tk visulaization vmd
Language:Tcl 2

pdb-files

horsicq / PDBRipper

BioPandas / biopandas

biotite-dev / biotite

mdtraj / mdtraj

HoShiMin / formatPE

project-gemmi / gemmi

molstar / VSCoding-Sequence

Biswa96 / PDBDownloader

microsoft / SQLCallStackResolver

jgreener64 / pdb-benchmarks

Broihon / Symbol-Parser

gu1729 / pdbdump

smx-smx / PDBSharp

PDB-REDO / libcifpp

SeanCline / PythonSymbols

a-r-j / CPDB

PombertLab / 3DFI

lucagl / MOAD_ligandFinder

mmagnus / emacs-pdb-mode

johnnytam100 / pdb2uniprot

Sarah-Hesham-2022 / Unity-Protein-Visualization

hocinebib / PisaPy

metaworm / pdb-viewer

project-gemmi / pdb-stats

ISDementyev / pmUE

OmerRaviv / PdbBenchmarks

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

jewettaij / dlpdb

mindleaving / genome-tools

moritzobenauer / ProjectRaccoon

shred / commons-pdb

continuous-symmetry-measure / pdb_prep

gkoulouras / seq-sec-ratio

project-gemmi / wasm

Spenhouet / PDBViewer

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