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protein

Here are 331 public repositories matching this topic...

biopython / biopython

Open

Define SeqFeature sub for integer offset

peterjc commented Jan 1, 2022

See https://github.com/biopython/biopython/blob/master/Bio/SeqFeature.py and __add__, need to do the same specifically for integer offsets.

Workaround feature + (-5) instead of feature - 5, see https://twitter.com/tomeraltman/status/1473764959347638273

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Enhancement good first issue

Open

silence warnings PDBConstructionWarning in test_PDB_StructureAlignment.py

4

Open

PAML run method docstrings - return value

16

Find more good first issues

mdshw5 / pyfaidx

Efficient pythonic random access to fasta subsequences

python bioinformatics genomics indexing dna protein fasta samtools bgzf

Updated Jan 31, 2022
Python

graphein

a-r-j / graphein

Sponsor

Open

Add additional inputs for CLI

a-r-j commented Mar 8, 2022

Describe the solution you'd like

inputs for chain selection as a separate .txt file
Input as list of PDB codes (txt file) rather than PDB directory path

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enhancement good first issue

Open

YAML Configs for existing methods

Open

Add distances as edge features

flowhub-team / awesome-omics

A collection of awesome things regarding all omics.

awesome genomics ngs protein omics single-cell ngs-pipeline wgs-analysis

Updated Mar 22, 2022

prody / ProDy

A Python Package for Protein Dynamics Analysis

python dynamics protein

Updated Apr 8, 2022
Python

fogleman / ribbon

Ribbon diagrams of proteins in #golang.

go chemistry protein-data-bank protein biochemistry 3d

Updated Feb 19, 2022
Go

haddocking / pdb-tools

A dependency-free cross-platform swiss army knife for PDB files.

python bioinformatics structural-biology pdb protein structural-bioinformatics utrecht-university rcsb

Updated Feb 8, 2022
Python

PeptoneInc / dspp-keras

Protein order and disorder data for Keras, Tensor Flow and Edward frameworks with automated update cycle made for continuous learning applications.

machine-learning database ai polymer biology tensorflow protein-structure keras prediction dataset protein amino-acids biotechnology

Updated Jun 29, 2017
Python

AngelRuizMoreno / Jupyter_Dock

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.

cheminformatics protein-structure jupyter-notebook computational-biology protein drug-discovery drug-repurposing rdkit openbabel drug-design mdanalysis autodock ledock molecular-docking autodock-vina py3dmol

Updated Nov 24, 2021
Jupyter Notebook

debbiemarkslab / EVcouplings

Evolutionary couplings from protein and RNA sequence alignments

protein structure-prediction 3d-structure protein-complexes

Updated Nov 1, 2021
Jupyter Notebook

bio4j / bio4j

Bio4j abstract model and general entry point to the project

java bioinformatics database graph proteins protein gene-ontology java-8 graph-database ncbi-taxonomy graph-databases property-graph graph-data uniprot bio4j graph-queries graph-schema titan bio4j-titan uniref

Updated Dec 16, 2016
Java

biologyguy / BuddySuite

Bioinformatics toolkits for manipulating sequence, alignment, and phylogenetic tree files

python workflow bioinformatics command-line biology dna protein phylogenetics alignment

Updated Dec 6, 2021
Python

Shen-Lab / DeepAffinity

Protein-compound affinity prediction through unified RNN-CNN

protein semi-supervised-learning drug-discovery attention-mechanism interpretable-deep-learning

Updated Jun 22, 2021
Python

ncbi / icn3d

web-based protein structure viewer and analysis tool interactively or in batch mode

nodejs delphi webgl jupyter-notebook chemical protein snp nucleotide structure-viewer 3d-structure 3d-viewer molecular-viewer icn3d protein-viewer

Updated Mar 29, 2022
JavaScript

lightdock

lightdock / lightdock

Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm

bioinformatics chemistry structural-biology molecular-structures protein-structure artificial-intelligence dna protein proteomics docking peptides molecular-biology protein-design protein-protein-interaction swarm-intelligence structural-bioinformatics protein-dna-interactions bioinformatics-tool glowworm-swarm-optimization protein-docking

Updated Mar 1, 2022
C

malllabiisc / ProteinGCN

ProteinGCN: Protein model quality assessment using Graph Convolutional Networks

deep-learning pytorch protein graph-convolutional-networks graph-neural-networks protein-model-quality-estimation

Updated Oct 27, 2020
Python

jgreener64 / mmterm

View proteins and trajectories in the terminal

visualization terminal protein-structure protein terminal-graphics trajectory

Updated Aug 8, 2020
Python

Rostlab / SeqVec

Modelling the Language of Life - Deep Learning Protein Sequences

bioinformatics protein-structure protein protein-function

Updated Sep 15, 2020
Python

j3xugit / RaptorX-Contact

Deep residual neural network for protein contact/distance prediction developed by Xu group

learning deep protein folding

Updated Sep 13, 2020
Python

swsoyee / r3dmol

Sponsor

🧬 An R package for visualizing molecular data in 3D

visualization r protein-structure computational-biology molecular-graphics protein computational-chemistry htmlwidgets hacktoberfest 3d molecular-modeling

Updated Sep 16, 2021
JavaScript

josiahseaman / FluentDNA

FluentDNA allows you to browse sequence data of any size using a zooming visualization similar to Google Maps. You can use FluentDNA as a standalone program or as a python module for your own bioinformatics projects.

visualization bioinformatics sequencing liftover dna protein alignment fasta fluent ddv msa fasta-sequences bioinformatics-tool chain-alignment fluentdna

Updated Jul 19, 2021
JavaScript

hiranumn / DeepAccNet

Pytorch/Python3 implementation of DeepAccNet, protein model accuracy evaluator.

pytorch protein ema pyrosetta

Updated Jun 18, 2021
Python

zjunlp / OntoProtein

Code and datasets for the ICLR2022 paper "OntoProtein: Protein Pretraining With Gene Ontology Embedding"

protein knowledge-graph gene-ontology bert protein-protein-interaction protein-function-prediction protein-structure-prediction protein-pretraining ontoprotein

Updated Apr 8, 2022
Python

food-nutrients / food-nutrients

🍴 Food Nutrients

food protein fat essential food-classification nutrients nutrition foods food-recommendation carbs minerals vitamins

Updated Apr 9, 2022
JavaScript

murphycj / AGFusion

Python package to annotate and visualize gene fusions.

python rna-seq cancer gene-fusion protein fusion chimera cancer-genomics

Updated Feb 22, 2022
Python

UCLOrengoGroup / cath-tools

Protein structure comparison tools such as SSAP and SNAP

bioinformatics biology pdb structure protein alignment score ssap orengo cath superposition ucl orengo-group taylor protein-structure-comparison cath-resolve-hits

Updated May 30, 2021
C++

psipred / cgdms

Differentiable molecular simulation of proteins with a coarse-grained potential

automatic-differentiation protein force-field potential coarse-grained

Updated Feb 21, 2022
Python

molstar / VSCoding-Sequence

VSCode Extension for interactively visualising protein structure data in the editor

structural-biology pdb protein-structure structure vscode molecule protein vscode-extension pdb-files molstar

Updated Feb 14, 2022
TypeScript

KirillKryukov / naf

Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences

compression dna file-format protein rna fasta fastq

Updated Mar 3, 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

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