JAEYOONSUNG

JAEYOONSUNG's Stars

• Ryan-Abramowitz/MoleculeBinding

  ML to predict which molecules bind to a protein

  Language:Python4

• POVME/POVME3

  A pocket volume analyzer for use in protein modeling.

  Language:Python489

• padlocbio/padloc

  Locate antiviral defence systems in prokaryotic genomes

  Language:R4810

• gaarangoa/ARGminer

  Curation of Antibiotic Resistance Genes by using crowdsourcing

  Language:CSS92

• WrightonLabCSU/DRAM

  Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

  Language:Python25852

• mdmparis/defense-finder

  Systematic search of all known anti-phage systems.

  Language:Python7913

• LinearDesignSoftware/LinearDesign

  The LinearDesign mRNA design software.

  Language:C++16557

• agemagician/ProtTrans

  ProtTrans is providing state of the art pretrained language models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

  Language:Jupyter Notebook1.1k154

• eggnogdb/eggnog-mapper

  Fast genome-wide functional annotation through orthology assignment

  Language:Python575106

• Superzchen/iFeatureOmega-GUI

  iFeatureOmega is a comprehensive platform for generating, analyzing and visualizing more than 170 representations for biological sequences, 3D structures and ligands. To the best of our knowledge, iFeatureOmega supplies the largest number of feature extraction and analysis approaches for most molecule types compared to other pipelines. Three versions (i.e. iFeatureOmega-Web, iFeatureOmega-GUI and iFeatureOmega-CLI) of iFeatureOmega have been made available to cater to both experienced bioinformaticians and biologists with limited programming expertise. iFeatureOmega also expands its functionality by integrating 15 feature analysis algorithms (including ten cluster algorithms, three dimensionality reduction algorithms and two feature normalization algorithms) and providing nine types of interactive plots for statistical features visualization (including histogram, kernel density plot, heatmap, boxplot, line chart, scatter plot, circular plot, protein three dimensional structure plot and ligand structure plot). iFeatureOmega is an open-source platform for academic purposes. The web server can be accessed through http://ifeature2.erc.monash.edu and the GUI and CLI versions can be download at: https://github.com/Superzchen/iFeatureOmega-GUI and https://github.com/Superzchen/iFeatureOmega-CLI, respectively.

  Language:Python256

• Superzchen/iFeature

  iFeature is a comprehensive Python-based toolkit for generating various numerical feature representation schemes from protein or peptide sequences. iFeature is capable of calculating and extracting a wide spectrum of 18 major sequence encoding schemes that encompass 53 different types of feature descriptors. Furthermore, iFeature also integrates five kinds of frequently used feature clustering algorithms, four feature selection algorithms and three dimensionality reduction algorithms.

  Language:Python18566

• Kuniz/alfnaversearch

  Naver Search Workflow for Alfred (알프레드 네이버 검색/사전/지도 자동완성 워크플로우)

  Language:Python21217

• sokrypton/ColabFold

  Making Protein folding accessible to all!

  Language:Jupyter Notebook2k504

• google-deepmind/alphafold

  Open source code for AlphaFold 2.

  Language:Python12.9k2.3k

• morgannprice/PaperBLAST

  PaperBLAST: find papers about a protein or its homologs

  Language:Perl356

• Pymol-Scripts/Pymol-script-repo

  Collected scripts for Pymol

  Language:Python449257

• opencobra/cobratoolbox

  The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

  Language:MATLAB253318

• ncbi/pgap

  NCBI Prokaryotic Genome Annotation Pipeline

  Language:Common Workflow Language31688

• PacificBiosciences/pbbioconda

  PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.

  25545

• veg/hyphy

  HyPhy: Hypothesis testing using Phylogenies

  Language:HyPhy22169