67 results found Sort:

biopython
biopython biopython
1.7k
4.2k
other
168
Official git repository for Biopython (originally converted from CVS)
dna python protein genomics biopython phylogenetics bioinformatics protein-structure sequence-alignment
Created 2009-03-15
15,817 commits to master branch, last one 20 hours ago
aqlaboratory
openfold aqlaboratory
460
2.6k
apache-2.0
46
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
pytorch alphafold2 protein-structure
Created 2021-09-14
1,447 commits to main branch, last one 8 days ago
a-r-j
graphein a-r-j
125
990
mit
19
Protein Graph Library
dgl rna python protein pytorch interactome ppi-networks deep-learning interactomics bioinformatics drug-discovery protein-design protein-data-bank protein-structure pytorch-geometric structural-biology computational-biology graph-neural-networks geometric-deep-learning gene-regulatory-networks
Created 2019-08-28
796 commits to master branch, last one 12 days ago
aqlaboratory
proteinnet aqlaboratory
130
850
mit
54
Standardized data set for machine learning of protein structure
dataset proteins deep-learning machine-learning protein-sequence protein-structure
Created 2018-03-10
192 commits to master branch, last one 3 years ago
BradyAJohnston
MolecularNodes BradyAJohnston
81
809
mit
16
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
pdb sciart blender protein molecule proteins biochemistry blender-addon visualisation geometry-nodes protein-data-bank protein-structure molecular-modeling structural-biology protein-visualization
Created 2022-04-25
1,516 commits to main branch, last one 3 days ago
BioPandas
biopandas BioPandas
117
691
bsd-3-clause
18
Working with molecular structures in pandas DataFrames
pdb mol2 molecule molecules pdb-files bioinformatics drug-discovery pandas-dataframe protein-structure molecular-structures computational-biology
Created 2015-11-21
355 commits to main branch, last one 8 months ago
steineggerlab
foldseek steineggerlab
92
675
gpl-3.0
21
Foldseek enables fast and sensitive comparisons of large structure sets.
alignments clustering bioinformatics protein-structure
Created 2019-01-21
984 commits to master branch, last one 8 days ago
songlab-cal
tape songlab-cal
130
634
bsd-3-clause
22
Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
dataset pytorch benchmark deep-learning language-modeling protein-sequences protein-structure semi-supervised-learning
Created 2019-12-09
344 commits to master branch, last one 2 years ago
biojava
biojava biojava
379
581
lgpl-2.1
79
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
pdb java genomics bioinformatics parser-library protein-data-bank protein-sequences protein-structure sequence-alignment structure-alignment protein-modification structural-bioinformatics
Created 2013-04-03
6,829 commits to master branch, last one 9 days ago
hpcaitech
FastFold hpcaitech
80
549
apache-2.0
17
Optimizing AlphaFold Training and Inference on GPU Clusters
gpu cuda pytorch evoformer alphafold2 parallelism habana-gaudi protein-folding protein-structure
Created 2022-02-27
103 commits to main branch, last one 10 months ago
soedinglab
hh-suite soedinglab
128
507
gpl-3.0
24
Remote protein homology detection suite.
cpp simd hhpred hhblits viterbi hh-suite hhsearch alignment opensource bioinformatics profile-search sequence-search protein-structure profile-profile-search
Created 2015-05-04
1,397 commits to master branch, last one 2 years ago
HannesStark
EquiBind HannesStark
110
464
mit
9
EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein
geometry proteins molecules equivariance drug-discovery protein-structure graph-neural-networks
Created 2021-10-26
36 commits to main branch, last one about a year ago
sacdallago
bio_embeddings sacdallago
63
439
mit
16
Get protein embeddings from protein sequences
pipeline embedders bio-embeddings language-model machine-learning protein-sequences protein-structure protein-prediction sequence-embeddings
Created 2019-04-10
1,282 commits to develop branch, last one about a year ago
pharmai
plip pharmai
98
412
gpl-2.0
15
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
pdb plip docker openbabel singularity bioinformatics python-bindings protein-structure scientific-computing
Created 2014-12-16
524 commits to master branch, last one 9 months ago
JuliaMolSim
Molly.jl JuliaMolSim
51
368
other
17
Molecular simulation in Julia
julia lennard-jones protein-structure molecular-dynamics physics-simulation molecular-simulation structural-bioinformatics
Created 2018-05-15
1,776 commits to master branch, last one 3 days ago
dptech-corp
Uni-Fold dptech-corp
63
350
apache-2.0
7
An open-source platform for developing protein models beyond AlphaFold.
pytorch alphafold deep-learning protein-structure alphafold-multimer
Created 2022-07-30
98 commits to main branch, last one 4 months ago
jonathanking
sidechainnet jonathanking
36
314
bsd-3-clause
9
An all-atom protein structure dataset for machine learning.
dataset deep-learning machine-learning protein-structure structural-biology
Created 2020-03-12
522 commits to master branch, last one 2 months ago
williamgilpin
pypdb williamgilpin
77
300
mit
20
A Python API for the RCSB Protein Data Bank (PDB)
pdb blast proteins proteomics protein-data-bank protein-sequences protein-structure
Created 2015-05-13
176 commits to master branch, last one 16 days ago
lightdock
lightdock lightdock
36
281
gpl-3.0
12
Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm
dna docking protein peptides chemistry proteomics bioinformatics protein-design protein-docking molecular-biology protein-structure structural-biology swarm-intelligence bioinformatics-tool molecular-structures artificial-intelligence protein-dna-interactions structural-bioinformatics glowworm-swarm-optimization protein-protein-interaction
Created 2019-09-27
488 commits to master branch, last one 4 months ago
tbepler
protein-sequence-embedding-iclr2019 tbepler
74
253
other
11
Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019
pytorch deep-learning language-model protein-modeling protein-sequence protein-embedding protein-structure recurrent-neural-networks protein-representation-learning
Created 2019-02-22
7 commits to master branch, last one 2 years ago
AngelRuizMoreno
Jupyter_Dock AngelRuizMoreno
65
246
mit
11
Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting file formats and analyzing the results.
rdkit ledock protein py3dmol autodock openbabel mdanalysis drug-design autodock-vina drug-discovery cheminformatics drug-repurposing jupyter-notebook molecular-docking protein-structure computational-biology
Created 2021-09-10
29 commits to main branch, last one 2 years ago
baaihealth
OpenComplex baaihealth
33
243
apache-2.0
17
Trainable PyTorch framework for developing protein, RNA and complex models.
pytorch alphafold2 rna-structure protein-structure
Created 2023-01-03
23 commits to master branch, last one 8 months ago
westlake-repl
SaProt westlake-repl
21
242
mit
5
Saprot: Protein Language Model with Structural Alphabet
protein foldseek alphafold2 pretraining protein-llm structure-aware protein-sequence protein-structure structural-alphbet predicted-structures protein-language-model representation-learning
Created 2023-10-02
97 commits to main branch, last one 9 days ago
rdk
p2rank rdk
32
227
mit
8
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.
pdb java mmcif pymol groovy ligand p2rank proteins binding-sites random-forest bioinformatics drug-discovery protein-surface machine-learning protein-structure virtual-screening molecular-structures protein-ligand-docking structural-bioinformatics protein-ligand-interactions
Created 2016-09-25
1,533 commits to develop branch, last one about a month ago
mattragoza
LiGAN mattragoza
44
208
gpl-2.0
6
Deep generative models of 3D grids for structure-based drug discovery
molgrid pytorch deep-learning drug-discovery generative-models protein-structure
Created 2018-04-20
858 commits to master branch, last one about a year ago
project-gemmi
gemmi project-gemmi
39
200
mpl-2.0
15
macromolecular crystallography library and utilities
cif mtz ccp4 mmcif pdb-files crystallography protein-structure structural-biology molecular-structures
Created 2017-02-02
4,107 commits to master branch, last one 3 days ago
opendilab
awesome-AI-based-protein-design opendilab
12
191
apache-2.0
2
A collection of research papers for AI-based protein design
awesome protein awesome-list protein-structure artificial-intelligence
Created 2022-11-07
14 commits to main branch, last one 19 days ago
biolib
openprotein biolib
54
177
mit
10
A PyTorch framework for prediction of tertiary protein structure
proteins protein-structure
Created 2018-09-08
163 commits to master branch, last one 3 years ago
adaptyvbio
ProteinFlow adaptyvbio
8
173
bsd-3-clause
7
Versatile computational pipeline for processing protein structure data for deep learning applications.
dataset deep-learning bioinformatics protein-design protein-data-bank protein-structure
Created 2023-02-15
1,309 commits to main branch, last one 3 months ago
napoles-uach
stmol napoles-uach
31
170
mit
5
This is the repository for the Stmol project, a Streamlit component that uses py3Dmol to render molecules.
molecular streamlit visualization protein-structure
Created 2020-07-29
160 commits to master branch, last one 5 months ago