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protein-sequence

Here are 36 public repositories matching this topic...

aqlaboratory / proteinnet

Standardized data set for machine learning of protein structure

machine-learning deep-learning proteins protein-structure dataset protein-sequence

Updated Nov 18, 2020
Python

tbepler / protein-sequence-embedding-iclr2019

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019

deep-learning protein-structure pytorch recurrent-neural-networks language-model protein-sequence protein-embedding protein-modeling protein-representation-learning

Updated Jun 16, 2021
Python

psipred / DMPfold

De novo protein structure prediction using iteratively predicted structural constraints

deep-learning protein-structure resnet protein-sequence protein-structure-prediction

Updated Jan 30, 2022
C

Shen-Lab / gcWGAN

Guided Conditional Wasserstein GAN for De Novo Protein Design

protein-structure protein generative-model generative-adversarial-networks protein-design protein-sequence

Updated Feb 23, 2021
Roff

proteinsolver

ostrokach / proteinsolver

Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.

bioinformatics structural-biology protein-structure protein protein-design protein-sequence graph-neural-networks

Updated Mar 24, 2021
Jupyter Notebook

cusbg / MolArt

MOLeculAR structure annoTator

visualization pdb protein-structure uniprot protein-sequence sequence-annotations protvista litemol

Updated Mar 26, 2022
JavaScript

MartinThoma / propy3

Sponsor

A Python 3 version of the protein descriptor package propy

python bioinformatics python3 protein-sequence dipeptide-composition-descriptors protein-descriptor geary-autocorrelation-descriptors

Updated Apr 14, 2022
Python

bhi-kimlab / DeepFam

Deep learning based alignment-free method for protein family modeling and prediction

deep-learning convolutional-neural-networks alignment-free protein-sequence

Updated Jul 31, 2018
Python

LPDI-EPFL / rstoolbox

Python Toolbox For Rosetta Silent Files Processing

science data-visualization data-analysis protein-design protein-sequence

Updated May 23, 2019
Python

jendelel / PrankWebApp

Web application for protein-ligand binding sites analysis and visualization

visualization web pdb protein-structure web-application conservation protein webapp analyses protein-ligand-interactions ligand protein-homology protein-sequence conservation-scores

Updated Apr 25, 2019
JavaScript

kn-bibs / dotplot

Simple visualisation tool for sequences' similarity in bioinformatics

bioinformatics visualisation gene-similarity protein-sequence dotplot

Updated Apr 12, 2018
Python

jaumebonet / RosettaSilentToolbox

Python Toolbox For Rosetta Silent Files Processing

science data-visualization data-analysis protein-design protein-sequence

Updated Aug 2, 2021
Python

IbrahimTanyalcin / I-PV

Interactive Protein Sequence VIsualization/Viewer - Interactive Circos

visualization viewer javascript-library interactive-visualizations amino-acid-sequence protein-sequence mutation-analysis

Updated Dec 14, 2021
HTML

COVID-Genome-Computational-Analysis

0xpranjal / COVID-Genome-Computational-Analysis

Computational predictions of protein attributes associated with COVID-19 using Data Science techniques

spike dna healthcare rna lzma sequence compressed kolmogorov-complexity protein-sequence 19 kolmogorov-smirnov glycoprotein sars covid sars-cov-2 rna-sequence covid-genome-ds complete-genome-analysis

Updated Jan 7, 2021
Jupyter Notebook

DSIMB / MEDUSA

A Deep Learning based protein flexibility prediction tool.

deep-learning prediction protein flexibility protein-sequence

Updated Apr 5, 2022
Perl

changlabtw / MS2CNN

convolutional-neural-networks protein-sequence ms-spectrum

Updated Apr 19, 2021
Python

leeneil / structure-generator

A machine learning model that builds amino acids into a protein model.

machine-learning structural-biology protein-structure computational-biology protein lstm gcn protein-sequence protein-structure-prediction graph-convolutional-network

Updated Apr 8, 2021
Python

zmmason / BINF

Computational programs and algorithms used to convert information from biochemical experiments (DNA/RNA/Protein/DNA chip/NGS) into useful information and data.

markov-chain motif dna fasta mass-spectrometry k-mer genome-analysis peptides de-bruijn-graphs fasta-sequences orf protein-sequence z-score directed-acyclic-graph overlap-graph cyclic-peptides cyclic-pattern

Updated Jan 28, 2021
Python

PeptoneInc / pepkalc

Robust simulation software for the comprehensive evaluation of protein electrostatics in unfolded state.

bioinformatics polymer simulation prediction protein biophysics protein-sequence electrostatics protonation

Updated Jan 31, 2019
Python

PNNL-Comp-Mass-Spec / protein-coverage-summarizer

Computes the percent of the residues in each protein sequence that have been identified, based on a list of identified peptides. A graphical user interface (GUI) is provided to allow the user to select the input files, set the options, and browse the coverage results.

protein-sequences fasta mass-spectrometry protein-sequence

Updated Apr 26, 2022
C#

Shen-Lab / Fold2Seq-icml2021

[ICML 2021] "Fold2Seq: A Joint Sequence(1D)-Fold(3D) Embedding-based Generative Model for Protein Design" by Yue Cao, Payel Das, Vijil Chenthamarakshan, Pin-Yu Chen, Igor Melnyk, Yang Shen

protein-structure transformer protein generative-model protein-design protein-sequence

Updated Jun 8, 2021
Python

ratvec / results

Results from application of RatVec to protein sequences

nlp kernel-methods representation-learning protein-sequence ratvec

Updated Apr 5, 2019
Jupyter Notebook

bateman-research / sequence-bias

Scripts to analyse the sequence composition and bias of protein and nucleotide sequences.

bioinformatics protein-sequence dna-sequence

Updated May 12, 2021
R

acgtun / hsearch

HSEARCH: fast and accurate protein sequence motif search and clustering

clustering locality-sensitive-hashing sequence-alignment motif-discovery protein-sequence

Updated Mar 23, 2017
C++

lukaszsobala / spike-annotation

Annotation of SARS-CoV-2 Spike glycoprotein

bioinformatics protein protein-sequence demogorgon protein-sequence-analysis covid-19 covid19 sars-cov-2

Updated Apr 28, 2020

mtp-usz / IsoAligner

IsoAligner: dynamic mapping of amino acid positions across protein isoforms

rest-api alternative-splicing ensemble webtool ucsc uniprot sequence-alignment protein-sequence refseq splice-variants exon-mapping protein-ids aminoacid-position protein-isoform

Updated May 4, 2022
Python

bateman-research / clustering-ssn

Scripts to calculate sequence similarity networks (SSNs) and clustering of protein sequences.

bioinformatics protein-sequence pfam protein-clustering

Updated May 14, 2021
R

haichengyi / bioseq2vec

BioSeq2vec: learning deep representation of biological sequences using LSTM Encoder-Decoder

lstm sequence-to-sequence representation-learning mirna lncrna biological-sequences encoder-decoder protein-sequence circrnas rna-sequence ncrna-protein-interactions

Updated Jun 6, 2021
Python

johnnytam100 / FPredX

FPredX

machine-learning bioinformatics protein-design protein-sequence protein-function-prediction

Updated Nov 5, 2021
Python

johnnytam100 / awesome-protein-design

A curated list of awesome protein design research, software and resources.

bioinformatics structural-biology protein-structure molecular-biology protein-design protein-protein-interaction protein-sequence structural-bioinformatics protein-engineering protein-folding protein-structure-prediction bioinformatics-tool protein-function alphafold alphafold2 alphafold-multimer

Updated May 10, 2022

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