83 results found Sort:

biopython
biopython biopython
1.8k
4.4k
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
15,956 commits to master branch, last one a day ago
aqlaboratory
openfold aqlaboratory
550
2.8k
apache-2.0
50
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
pytorch alphafold2 protein-structure
Created 2021-09-14
1,467 commits to main branch, last one 6 days ago
sokrypton
ColabFold sokrypton
496
2.0k
mit
47
Making Protein folding accessible to all!
bioinformatics protein-structure structure-prediction multiple-sequence-alignment
Created 2021-07-19
1,331 commits to main branch, last one 2 days ago
a-r-j
graphein a-r-j
132
1.0k
mit
18
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
807 commits to master branch, last one 28 days ago
BradyAJohnston
MolecularNodes BradyAJohnston
87
916
gpl-3.0
19
Toolbox for molecular animations in Blender, powered by Geometry Nodes.
pdb sciart blender protein molecule proteins molecular biochemistry blender-addon visualisation geometry-nodes protein-data-bank protein-structure molecular-dynamics molecular-graphics molecular-modeling structural-biology protein-visualization
Created 2022-04-25
1,739 commits to main branch, last one 10 days ago
aqlaboratory
proteinnet aqlaboratory
132
864
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 4 years ago
steineggerlab
foldseek steineggerlab
102
830
gpl-3.0
18
Foldseek enables fast and sensitive comparisons of large structure sets.
alignments clustering bioinformatics protein-structure
Created 2019-01-21
1,256 commits to master branch, last one 13 days ago
BioPandas
biopandas BioPandas
121
715
bsd-3-clause
17
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
360 commits to main branch, last one 3 months ago
songlab-cal
tape songlab-cal
129
664
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 3 years ago
biojava
biojava biojava
388
594
lgpl-2.1
78
: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
6,856 commits to master branch, last one 2 months ago
hpcaitech
FastFold hpcaitech
86
574
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 about a year ago
soedinglab
hh-suite soedinglab
134
542
gpl-3.0
25
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
1,398 commits to master branch, last one 13 days ago
HannesStark
EquiBind HannesStark
109
482
mit
8
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 2 years ago
sacdallago
bio_embeddings sacdallago
65
468
mit
15
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 2 years ago
pharmai
plip pharmai
107
464
gpl-2.0
16
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 about a year ago
JuliaMolSim
Molly.jl JuliaMolSim
54
405
other
18
Molecular simulation in Julia
julia lennard-jones protein-structure molecular-dynamics physics-simulation molecular-simulation structural-bioinformatics
Created 2018-05-15
1,902 commits to master branch, last one 2 days ago
dptech-corp
Uni-Fold dptech-corp
74
378
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 10 months ago
westlake-repl
SaProt westlake-repl
33
354
mit
6
Saprot: Protein Language Model with Structural Alphabet (AA+3Di)
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
124 commits to main branch, last one 2 days ago
jonathanking
sidechainnet jonathanking
38
339
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 8 months ago
williamgilpin
pypdb williamgilpin
75
314
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
181 commits to master branch, last one 3 months ago
lightdock
lightdock lightdock
42
307
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 10 months ago
baaihealth
OpenComplex baaihealth
33
264
apache-2.0
17
Trainable PyTorch framework for developing protein, RNA and complex models.
pytorch alphafold2 rna-structure protein-structure
Created 2023-01-03
24 commits to master branch, last one 8 days ago
AngelRuizMoreno
Jupyter_Dock AngelRuizMoreno
67
259
mit
12
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
tbepler
protein-sequence-embedding-iclr2019 tbepler
75
258
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 3 years ago
rdk
p2rank rdk
34
251
mit
9
P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.
pdb java mmcif pymol groovy p2rank docking chimerax proteins binding-sites bioinformatics drug-discovery machine-learning protein-structure virtual-screening molecular-structures computational-biology protein-ligand-docking structural-bioinformatics protein-ligand-interactions
Created 2016-09-25
1,695 commits to develop branch, last one 7 days ago
adaptyvbio
ProteinFlow adaptyvbio
17
242
bsd-3-clause
8
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 9 months ago
project-gemmi
gemmi project-gemmi
45
231
mpl-2.0
17
macromolecular crystallography library and utilities
cif mtz ccp4 mmcif pdb-files crystallography protein-structure structural-biology molecular-structures
Created 2017-02-02
4,286 commits to master branch, last one a day ago
opendilab
awesome-AI-based-protein-design opendilab
14
229
apache-2.0
3
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 6 months ago
mattragoza
LiGAN mattragoza
44
225
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
rcedgar
muscle rcedgar
23
213
gpl-3.0
6
Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and pre...
biology algorithms bioinformatics sequence-search protein-alignment protein-structure sequence-clustering nucleotide-alignment protein-structure-alignment
Created 2021-06-19
259 commits to main branch, last one 3 days ago