mmcif

There are 0 repository under mmcif topic.

p2rank
rdk / p2rank
P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.
bioinformatics machine-learning protein-structure pdb binding-sites proteins ligand protein-surface structural-bioinformatics protein-ligand-interactions java random-forest mmcif pymol groovy protein-ligand-docking molecular-structures drug-discovery virtual-screening p2rank
Language:Groovy 234
project-gemmi / gemmi
macromolecular crystallography library and utilities
cif mmcif crystallography protein-structure molecular-structures ccp4 pdb-files structural-biology mtz
Language:C++ 206
douweschulte / pdbtbx
A library to open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files in Rust.
crystallography rust rust-crate pdb pdb-parser pdbx-files scientific atoms mmcif
Language:Rust 49
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 40
PDB-REDO / libcifpp
Library containing code to manipulate mmCIF and PDB files
mmcif pdb-files protein-structure
Language:C++ 27
MooersLab / jupyterlabpymolpysnips
Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.
jupyter jupyter-notebook jupyterlab notebook python snippets grayscale ribbon-diagram protein-structure rna-structure dna-structure molecular-representation literate-programming moleclar-graphics pdb mmcif ligand biomolecular molecular
Language:HTML 22
ihmwg / IHMCIF
📖 mmCIF support for hybrid/integrative models
mmcif pdb hybrid-model dictionary integrative-modeling
Language:Shell 21
refresh-bio / protestar
Protein Structure Archiver
alphafold compression mmcif pdb proteins
Language:C++ 12
project-gemmi / periodic-table
Search PDB by elements.
mmcif pdb periodic-table
Language:JavaScript 10
biomadeira / BioDownloader
📦 A Command Line Tool for downloading protein structures, sequences and MSAs
bioinformatics cli mmcif fasta gff sifts pfam cath pdb
Language:Python 9
MooersLab / orgpymolpysnips
Supports the use of PyMOL in literate programming in org-mode, which is best run in Emacs.
org-mode emacs literate-programming pymol molecular-graphics org-babel emacs-jupyter pdb protein mmcif
Language:YASnippet 7
MolDF
Ruibin-Liu / MolDF
Super lightweight and fast mmCIF/PDB/MOL2 file parser into Pandas DataFrames and backwards writer.
bioinformatics pandas pdb-parser mmcif mol2 python atomselection
Language:Python 7
AHoJ-project
cusbg / AHoJ-project
:wave: Webserver & command-line tool for search of APO (unbound) protein structures from HOLO (bound) forms and vice versa. http://apoholo.cz
bioinformatics alignment python pymol molstar structural-bioinformatics pdb mmcif rest-api webapp apo-holo fastapi protein-structure proteins protein-data-bank structural-biology protein-ligand-complex computational-biology drug-discovery
6
Joseph-Ellaway / Ramachandran_Plotter
Program to plot a Ramachandran plot of all dihedral angles from a given PDB file. Background is empirically generated from the peptides in the Top8000 PDB data set.
dihedral-angles ramachandran-plot peptides plot modern mmcif pdb protein-data-bank protein-structure ramachandran structural-biology
Language:Python 6
justinmc / tiny-molecule
A small, developer-friendly 3D molecule viewer for the modern web
molecule pdb mmcif visualizer 3d
Language:JavaScript 4
project-gemmi / mmcif-benchmark
Benchmarks for reading and interpreting mmCIF files
mmcif benchmark pdb-database protein-structure
Language:Python 4
bartongroup / ProteoFAV
Open-source framework for simple and fast integration of protein structure data with sequence annotations and genetic variation
annotations bioinformatics data-analysis dssp features mmcif pandas pdb python sifts structural-biology variants
Language:Python 3
berrisfordjohn / adding_stats_to_mmcif
Program to add sequences and data collection statistics to mmCIF files for PDB deposition
mmcif pdb ccp4 crystallography
Language:Python 2
haddocking / haddock-mmcif
Encode information from a HADDOCK run to a cif file to be deposited in PDB-Dev.
pdb haddock mmcif pdb-dev utrecht-university
Language:Python 2
project-gemmi / wasm
Parts of Gemmi in WebAssembly.
pdb-files mmcif wasm
Language:HTML 2
JMB-Scripts / CIF-to-PDB
Convert in batch CIF files to PDB
cif mmcif pdb pdb-files
Language:Python 1
multimeric / mmcifix
Fixes mmCIF protein structure files
bioinformatics structural-biology crystallography pdb-database mmcif
Language:Python 1
samuellimce / pdbx
A PDBx/mmCIF-format parser and extractor.
structural-biology computational-biology computational-chemistry bioinformatics cheminformatics pdb pdbx mmcif hacktoberfest
1
yokochi47 / pdbx-validation
The pdbx-validation is a generation tool of alternative wwPDB validation reports
pdb validation mmcif pdbml rdf owl
Language:HTML 1
riboxyz
rtviii / riboxyz
Datatypes for the ribosome.
cryoem hidden-markov-model mmcif pdb ribosome structural-biology types
Language:C 0
amaurypm / struct2seq
Extract chains' and polypeptides' sequences from PDB or mmCIF files.
bioinformatics pdb mmcif sequence fasta
Language:Python

mmcif

rdk / p2rank

project-gemmi / gemmi

douweschulte / pdbtbx

jgreener64 / pdb-benchmarks

PDB-REDO / libcifpp

MooersLab / jupyterlabpymolpysnips

ihmwg / IHMCIF

refresh-bio / protestar

project-gemmi / periodic-table

biomadeira / BioDownloader

MooersLab / orgpymolpysnips

Ruibin-Liu / MolDF

cusbg / AHoJ-project

Joseph-Ellaway / Ramachandran_Plotter

justinmc / tiny-molecule

project-gemmi / mmcif-benchmark

bartongroup / ProteoFAV

berrisfordjohn / adding_stats_to_mmcif

haddocking / haddock-mmcif

project-gemmi / wasm

JMB-Scripts / CIF-to-PDB

multimeric / mmcifix

samuellimce / pdbx

yokochi47 / pdbx-validation

rtviii / riboxyz

amaurypm / struct2seq