38 results found Sort:

songlab-cal
tape songlab-cal
130
673
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
LirongWu
awesome-protein-representation-learning LirongWu
72
624
mit
24
Awesome Protein Representation Learning
protein-modeling protein-embedding protein-sequences representation-learning protein-representation-learning
Created 2022-10-05
69 commits to main branch, last one about a month ago
biojava
biojava biojava
391
595
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 3 months ago
microsoft
evodiff microsoft
76
539
mit
15
Generation of protein sequences and evolutionary alignments via discrete diffusion models
generative-model protein-sequences discrete-diffusion multiple-sequence-alignment
Created 2022-06-07
479 commits to main branch, last one 2 months ago
sacdallago
bio_embeddings sacdallago
66
472
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
williamgilpin
pypdb williamgilpin
75
316
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 4 months ago
lucidrains
protein-bert-pytorch lucidrains
22
153
mit
8
Implementation of ProteinBERT in Pytorch
deep-learning protein-sequences unsupervised-learning artificial-intelligence
Created 2021-05-26
20 commits to main branch, last one 3 years ago
oxpig
AbLang oxpig
24
129
bsd-3-clause
3
AbLang: A language model for antibodies
semantic antibodies language-model protein-sequences
Created 2021-12-31
42 commits to main branch, last one about a year ago
songlab-cal
tape-neurips2019 songlab-cal
34
118
mit
9
Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. (DEPRECATED)
dataset benchmark deep-learning language-modeling protein-sequences protein-structure semi-supervised-learning
Created 2019-06-19
88 commits to master branch, last one 3 years ago
flatironinstitute
deepblast flatironinstitute
21
114
bsd-3-clause
6
Neural Networks for Protein Sequence Alignment
protein neural-networks language-modeling protein-sequences protein-structure sequence-alignment structural-alignments
Created 2020-06-04
367 commits to master branch, last one about a month ago
debbiemarkslab
plmc debbiemarkslab
37
106
mit
9
Inference of couplings in proteins and RNAs from sequence variation
protein-sequences protein-structure undirected-graphs protein-interaction sequence-alignments
Created 2016-01-09
52 commits to master branch, last one about a year ago
rcedgar
usearch12 rcedgar
12
104
gpl-3.0
5
Open-source usearch
bioinformatics protein-alignment protein-sequences search-algorithms nucleotide-alignment computational-biology bioinformatics-algorithms
Created 2024-02-16
214 commits to master branch, last one 6 months ago
tbepler
prose tbepler
20
99
other
3
Multi-task and masked language model-based protein sequence embedding models.
deep-learning language-model protein-embedding protein-sequences sequence-embedding representation-learning
Created 2021-05-20
2 commits to main branch, last one 3 years ago
J-SNACKKB
FLIP J-SNACKKB
14
95
afl-3.0
7
A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design
protein protein-design protein-sequences representation-learning protein-fitness-prediction protein-function-prediction
Created 2021-05-13
178 commits to main branch, last one 4 months ago
pengzhangzhi
faplm pengzhangzhi
6
94
mit
3
FAPLM: A Drop-in Efficient Pytorch Implementation of Protein Language Models
pytorch protein-sequences protein-language-model
Created 2024-11-29
29 commits to main branch, last one 7 days ago
psipred
protein-vae psipred
17
81
mit
5
Variational autoencoder for protein sequences - add metal binding sites and generate sequences for novel topologies
topologies autoencoder protein-sequences protein-structure variational-autoencoder metal-binding-prediction
Created 2018-06-15
51 commits to master branch, last one 5 years ago
dosorio
Peptides dosorio
21
81
unknown
4
An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.
cran qsar peptides bioinformatics calculate-indices protein-sequences
Created 2014-02-07
469 commits to master branch, last one about a year ago
seqan
lambda seqan
20
77
other
13
LAMBDA – the Local Aligner for Massive Biological DatA
blast seqan alignment metagenomics ncbi-taxonomy bioinformatics blast-searches high-performance protein-sequences
Created 2015-06-22
759 commits to lambda3 branch, last one 3 months ago
pymodproject
pymod pymodproject
18
73
lgpl-2.1
8
PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.
pymol pymol-plugin bioinformatics homology-modeling protein-sequences protein-structures sequence-alignments similarity-searches structural-alignments
Created 2016-04-04
74 commits to master branch, last one 6 months ago
sbl-sdsc
mmtf-pyspark sbl-sdsc
27
68
apache-2.0
8
Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.
binder jupyter pyspark big-data apache-spark jupyter-notebook machine-learning protein-data-bank protein-sequences protein-structure scientific-computing protein-ligand-interactions protein-protein-interaction
Created 2017-05-11
1,752 commits to master branch, last one about a year ago
paulstothard
sequence_manipulation_suite paulstothard
23
64
gpl-3.0
3
A collection of simple JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. The Sequence Manipulation Suite is commonly used by molecular biologists, for teac...
dna-processing molecular-biology protein-sequences sequence-analysis
Created 2020-06-10
32 commits to master branch, last one about a month ago
nf-core
proteinfold nf-core
42
64
mit
163
Protein 3D structure prediction pipeline
nf-core nextflow pipeline workflow alphafold2 protein-folding protein-sequences protein-structure protein-fold-prediction
Created 2022-03-03
767 commits to master branch, last one 4 months ago
eliberis
parapred eliberis
15
59
mit
3
Paratope Prediction using Deep Learning
lstm python neural-network machine-learning protein-sequences protein-structure lstm-neural-networks
Created 2017-01-05
99 commits to master branch, last one 5 years ago
sagnikbanerjee15
Finder sagnikbanerjee15
14
58
mit
5
A fully automated gene annotator from RNA-Seq expression data
gtf finder rna-seq gene-models transcripts predict-genes bioinformatics gene-annotations genome-annotation protein-sequences changepoint-detection bioinformatics-pipeline gene-annotation-pipeline
Created 2021-01-08
189 commits to master branch, last one about a year ago
PKU-YuanGroup
TaxDiff PKU-YuanGroup
8
57
mit
5
The official code for "TaxDiff: Taxonomic-Guided Diffusion Model for Protein Sequence Generation"
ai4science generate-model meachine-learning protein-sequences
Created 2024-02-26
54 commits to main branch, last one 4 months ago
prescient-design
lobster prescient-design
8
55
apache-2.0
5
Lbster: Language models for Biological Sequence Transformation and Evolutionary Representation
plm bioml biology protein-sequences
Created 2024-02-19
53 commits to main branch, last one 10 days ago
ljvmiranda921
gym-lattice ljvmiranda921
8
54
mit
3
An HP 2D Lattice Environment with a Gym-like API for the Protein Folding Problem
python hp-model environments machine-learning protein-sequences protein-structure reinforcement-learning
Created 2018-04-03
83 commits to master branch, last one 2 years ago
OpenProteinAI
PoET OpenProteinAI
3
53
mit
3
Inference code for PoET: A generative model of protein families as sequences-of-sequences
proteins deep-learning generative-model protein-sequences protein-engineering protein-language-model
Created 2023-10-28
8 commits to main branch, last one 8 months ago
nanxstats
protr nanxstats
13
52
other
6
🧬 Toolkit for generating various numerical features of protein sequences
peptides bioinformatics machine-learning protein-sequences sequence-analysis feature-extraction feature-engineering
Created 2012-11-18
335 commits to master branch, last one 3 months ago
Genentech
walk-jump Genentech
8
49
apache-2.0
6
Official repository for discrete Walk-Jump Sampling (dWJS)
antibody proteins protein-design machine-learning protein-sequences
Created 2023-05-26
35 commits to main branch, last one about a year ago