Structural Bioinformatics Laboratory

Repositories

• mmtf-genomics

  Methods for mapping genomic data onto 3D protein structure.

  binder genomics protein-data-bank protein-structure pyspark mutations dbsnp
  Jupyter Notebook Apache-2.0 9 22 0 0 Updated Oct 19, 2020

• mmtf-pyspark

  Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

  machine-learning big-data binder apache-spark jupyter protein-data-bank protein-structure
  Python Apache-2.0 21 59 8 0 Updated May 18, 2020

• coronavirus-knowledge-graph

  OBSOLETE: Prototype Neo4j Knowledge Graph for Coronavirus outbreaks

  binder jupyter-notebook coronavirus coronavirus-analysis covid-19
  Jupyter Notebook MIT 11 12 0 0 Updated Apr 13, 2020

• mmtf-proteomics

  Methods for mapping proteomics data on 3D protein structure.

  binder protein-data-bank jupyter-notebook pyspark proteomics
  Jupyter Notebook Apache-2.0 1 12 0 0 Updated Jan 18, 2020

• sifts-columnar

  Benchmark and demo of representing SIFTS UniProt to PDB mappings in columnar data formats.
  Jupyter Notebook Apache-2.0 0 1 0 0 Updated Dec 14, 2019

• mmtf-workshop-2018

  Structural Bioinformatics Training Workshop & Hackathon 2018

  machine-learning big-data binder apache-spark jupyter hackathon protein-data-bank
  Jupyter Notebook Apache-2.0 27 48 2 0 Updated May 7, 2019

• mmtf-pyspark-benchmarks

  Benchmarks for mmtf-pyspark project
  Jupyter Notebook MIT 1 0 0 0 Updated Feb 11, 2019

• mmtf-spark

  Methods for the parallel and distributed analysis and mining of the Protein Data Bank using MMTF and Apache Spark.

  machine-learning big-data apache-spark protein-data-bank protein-structure scientific-computing protein-sequences
  Java Apache-2.0 35 20 9 0 Updated Feb 1, 2019

• biojava-notebooks

  BioJava examples in Jupyter Notebooks

  bioinformatics pdb protein-data-bank protein-structure jupyter-notebook biojava jupyter-lab
  Jupyter Notebook MIT 1 6 1 0 Updated Dec 20, 2018

• mmtf-hackathon-2018

  Hackathon projects repository for MMTF Workshop 2018
  Jupyter Notebook Apache-2.0 16 9 0 0 Updated Aug 30, 2018

• mmtf-data

  Data files for mmtf projects
  MIT 0 0 0 0 Updated Aug 14, 2018

• metal-binding-prediction

  Methods to predict metal binding sites in a protein by its amino acid sequence
  Jupyter Notebook 2 4 0 0 Updated Jun 15, 2018

• mm-dev

  Repository for the development of new methods for the mmtf-spark project
  Java 1 2 0 0 Updated Mar 31, 2018

• mmtf-workshop-2017

  Structural Bioinformatics Training Workshop & Hackathon 2017
  HTML Apache-2.0 38 16 0 0 Updated Jan 23, 2018

• QuickStructureSearch

  Forked from h3yin/QuickStructureSearch

  Obsolete student projects: Methods for fast structural database searches and clustering
  Java LGPL-2.1 6 2 0 0 Updated Feb 14, 2017

• structurecodec

  Forked from pwrose/structurecodec

  Obsolete project: Provides high-density compression and decompression of biomolecular structures.
  Java LGPL-2.1 3 2 0 0 Updated Nov 16, 2015