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protein-data-bank

Here are 31 public repositories matching this topic...

biojava / biojava

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☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

java bioinformatics genomics pdb parser-library protein-data-bank protein-structure protein-sequences sequence-alignment protein-modification structure-alignment structural-bioinformatics

Updated Jul 24, 2020
Java

fogleman / ribbon

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Ribbon diagrams of proteins in #golang.

go chemistry protein-data-bank protein biochemistry 3d

Updated Nov 1, 2019
Go

williamgilpin / pypdb

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A Python API for the RCSB Protein Data Bank (PDB)

proteins pdb protein-data-bank protein-structure protein-sequences proteomics blast

Updated Jun 9, 2020
Python

rasbt / protein-science

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A collection of useful tutorials for Protein Science

python protein-data-bank protein-science

Updated Jun 29, 2015
Python

a-r-j / graphein

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Protein Graph Library

bioinformatics deep-learning structural-biology protein-data-bank protein-structure computational-biology pytorch protein protein-design geometric-deep-learning graph-neural-networks dgl

Updated Jul 27, 2020
Jupyter Notebook

sbl-sdsc / mmtf-pyspark

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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 jupyter-notebook pyspark scientific-computing protein-sequences protein-protein-interaction protein-ligand-interactions

Updated May 18, 2020
Python

sbl-sdsc / mmtf-workshop-2018

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Structural Bioinformatics Training Workshop & Hackathon 2018

machine-learning big-data binder apache-spark jupyter hackathon protein-data-bank jupyter-notebook pyspark workshop-materials 3d-visualization protein-protein-interaction protein-ligand-interactions

Updated May 7, 2019
Jupyter Notebook

rcsb / mmtf

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The specification of the MMTF format for biological structures

bioinformatics compression protein-data-bank protein-structure file-format biological-structures

Updated May 13, 2019
Shell

sbl-sdsc / mmtf-spark

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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 protein-protein-interaction protein-ligand-interactions

Updated Feb 1, 2019
Java

BioHaskell / hPDB

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PDB parser in Haskell

haskell pdb protein-data-bank protein-structure file-format hackage pdb-parser

Updated Jan 28, 2019
Haskell

sbl-sdsc / mmtf-genomics

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Methods for mapping genomic data onto 3D protein structure.

binder genomics protein-data-bank protein-structure pyspark mutations dbsnp protein-protein-interaction protein-ligand-interactions cyverse protein-drug-interactions mmtf-pyspark

Updated Jun 29, 2020
Jupyter Notebook

sbl-sdsc / mmtf-proteomics

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Methods for mapping proteomics data on 3D protein structure.

binder protein-data-bank jupyter-notebook pyspark proteomics

Updated Jan 18, 2020
Jupyter Notebook

sbl-sdsc / biojava-notebooks

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BioJava examples in Jupyter Notebooks

bioinformatics pdb protein-data-bank protein-structure jupyter-notebook biojava jupyter-lab beakerx

Updated Dec 20, 2018
Jupyter Notebook

sarisabban / VaxDesign

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A script that computationally designs a vaccine

protein-data-bank protein-structure scaffold motif ab-initio receptor vaccine scaffold-protein covid-19 sars-cov-2

Updated May 10, 2020
Python

flatironinstitute / DeepFRI

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Deep functional residue identification

machine-learning deep-learning tensorflow protein-data-bank gene-ontology graph-convolutional-networks class-activation-maps

Updated Jul 14, 2020
Python

project-gemmi / pdb-stats

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Clickable PDB statistics: synchrotrons and MX software

statistics protein-data-bank synchrotron cross-filter x-ray-crystallography pdb-files

Updated Mar 17, 2020
HTML

FlavoInformatics / flavin_fun

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Analysis of Protein-Flavin Interactions that Control Chemical Reactivity

atom bioinformatics chemistry proteins protein-data-bank angstrom

Updated Apr 15, 2018
Jupyter Notebook

Spenhouet / PDBViewer

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Visualization of proteins directly from the PDB database or from a .pdb file.

pdb protein-data-bank protein pdb-files 3d-viewer pdb-database

Updated Feb 9, 2018
Java

gkoulouras / seq-sec-ratio

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A console application for the estimation of the primary and secondary structure's elements. Input should be the FASTA-formatted "ss.txt" file generated by PDB database.

bioinformatics pdb protein-data-bank protein-sequences vb-net bioinformatics-data amino-acids secondary-structure bioinformatics-scripts bioinformatics-databases pdb-files ss-txt protein-secondary-structure

Updated May 8, 2019
Visual Basic

matheuspokkkk / ppdistance

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defines the interface region of a protein complex making possible to calculate the i_rmsd between native and predicted structures following the CAPRI criteria

pdb protein-data-bank protein-structure protein protein-interaction protein-protein-interaction pdb-files

Updated May 11, 2018
C

pfgherardini / superpose3D

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Superpose3D is a software for local comparison of protein structures that allows for user-defined structure representations

bioinformatics structural-biology evolution protein-data-bank protein-structure comparison

Updated May 6, 2015
C++

RudoRoemer / PDB2MovieWeb

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Web-based front- and backend for PDB2Movie scripts

biology dynamics protein-data-bank protein-structure biochemistry protein-sequences physics-simulation flexibility

Updated Oct 10, 2018
PHP

svletana / Protein-analysis-using-pytraj

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Some miscellaneous scripts I made to do protein analysis using the pytraj library

python bioinformatics protein-data-bank

Updated Jan 5, 2019
Python

peterpaohuang / tapir

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A Python Framework for Integrating Classical and Quantum Mechanical Simulation Data, Experimental Data, and Cheminformatics into a Unified Predictive Engine for Macromolecular Design

python machine-learning automation protein-data-bank scikit-learn webscraper data-visualization data-analysis smiles experimental-data chemical-descriptors thermo-physical-descriptors polymer-db

Updated Jan 16, 2020
Python

ercanersoy / lsprotein

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Protein lister on command line interface

python cli command-line pdb rest-api protein-data-bank python3 protein lister ls command-line-interface protein-database

Updated May 7, 2020
Python

georgewatson / pdb_objects

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Object-oriented processing of PDB files in Python

python structural-biology pdb protein-data-bank

Updated Jun 7, 2019
Python

helykopter8484 / Protein_Data_Bank_Analysis

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pdb protein-data-bank biopython center-of-mass-protein-structure gene-ontology-from-pdb-file pfam-pdb-file

Updated Mar 12, 2018
Python

writ3it / AI_ProteinAnalysis

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Basic analysis of ligands extracted from structures described in Protein Data Bank

r analysis protein-data-bank ligands-extracted

Updated Dec 11, 2018
R

AMarinhoSN / lPDBmngr

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local PDB manager

structural-biology protein-data-bank protein-structure structural-bioinformatics

Updated Jan 15, 2020
Python

dmyersturnbull / atom-tin

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Tiny Scala API to stream, parse, and cache atom coordinates from Protein Data Bank files

streaming bioinformatics parse pdb protein-data-bank

Updated Sep 10, 2016
Scala

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