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pdb-files

Here are 40 public repositories matching this topic...

mdtraj / mdtraj

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An open library for the analysis of molecular dynamics trajectories

python pdb molecular-dynamics dihedral-angles mdtraj rmsd pdb-files molecular-dynamics-trajectories

Updated Jul 29, 2020
C

rasbt / biopandas

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Working with molecular structures in pandas DataFrames

bioinformatics pdb molecular-structures pandas-dataframe protein-structure molecule computational-biology drug-discovery molecules mol2 pdb-files

Updated Jun 14, 2020
HTML

horsicq / PDBRipper

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PDBRipper is a utility for extract an information from PDB-files.

pdb reverse-engineering pdb-files pdb-parser

Updated Jul 3, 2020
C++

haddocking / pdb-tools

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

python bioinformatics structural-biology pdb protein pdb-files

Updated Jun 8, 2020
Python

project-gemmi / gemmi

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macromolecular crystallography library and utilities

structural-biology molecular-structures protein-structure crystallography cif ccp4 mmcif pdb-files mtz

Updated Jul 30, 2020
C++

Biswa96 / PDBDownloader

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Standalone program to download PDB Symbol files for debugging without WDK

c windows pdb reverse-engineering reversing pdb-files pdb-database

Updated Jun 20, 2019
C

jgreener64 / pdb-benchmarks

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Benchmarking common tasks on proteins in various languages and packages

bioinformatics pdb comparison benchmarks mmcif structural-bioinformatics mmtf pdb-files

Updated Jun 17, 2020
Python

smx-smx / PDBSharp

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Fast and cross-platform parser for Microsoft PDB files

microsoft parser library csharp debug microsoft-pdb debug-symbols pdb-files pdb-parser

Updated Mar 14, 2020
C#

mmagnus / emacs-pdb-mode

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pdb-mode is an emacs-lisp minor mode for Emacs to perform a number of useful editing functions on Protein DataBank (PDB) formatted files. XEmacs and/or GNU Emacs are available for most computing platforms.

pdb rna-structure rna-pdb rna-structure-prediction pdb-files

Updated Apr 18, 2020
Emacs Lisp

SeanCline / PythonSymbols

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A WinDbg symbol server for all recent versions of CPython.

python pdb windbg pdb-files

Updated Jul 27, 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

mindleaving / genome-tools

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Tools for exploration and analysis of biochemical data like genomics and proteins

genomics pdb molecular-structures molecule molecular-dynamics molecular-simulation genomic-data-analysis genomics-visualization pdb-files peptide

Updated Apr 13, 2020
C#

shred / commons-pdb

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Read PalmOS PDB files with Java

java library palmos pdb-files

Updated Jan 26, 2019
Java

jewettaij / dlpdb

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collect statistics from the entire PDB library

structural-bioinformatics pdb-files

Updated May 23, 2020
Python

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

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

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

sagivba / pdb_prep

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PDB file parser and prepare tools.

chemistry proteins python3 pdb-files rscb

Updated Jun 20, 2020
Python

kabhel / DSSP_implt

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Programming project (Python) - Implementation of the DSSP method (Secondary Structure Assignment)

dssp python3-6 pdb-files

Updated Sep 20, 2018
Python

mmp1100000 / pyRosetta

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pyRosseta Workshop

python docking folding pdb-files

Updated Jun 6, 2018
Jupyter Notebook

dmflab / property_to_Bfac

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Simple awk script to transfer properties indexed by amino acid type to a Bfactor column of the pdb file.

structural-biology x-ray-crystallography pdb-files

Updated Aug 8, 2017
Awk

mitradip-das / data-analysis-md

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Data Analysis of MD Simulation

analysis rdf pdb molecular-dynamics molecular-dynamics-simulation data-analysis interaction msd tcf pdb-files radial-distribution-function interaction-dynamics niser bhubaneswar mean-square-displacement time-correlation-function interaction-statistics non-covalent-interactions

Updated Feb 4, 2018
C++

helykopter8484 / Ion_Environments_Project

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pdb biopython subprocess pdb-files ion-environments

Updated Mar 12, 2018
Python

holcombddf / Protein-Design-Scripts

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Scripts to aid protein design. Mostly parsing PDBs, fasta files, and score files.

protein fasta-sequences pdb-files score-files

Updated Feb 14, 2019
Python

continuous-symmetry / pdbslicer

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Bisect protein file (PDB) into sub units (i.e amino acids)

bioinformatics chemistry pdb pdb-files

Updated Dec 31, 2018
Perl

ExhoAR22 / pdbutil

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Utility & library for working with PDB files

c library pdb pdb-files pdb-parser

Updated Jul 10, 2020
C

Broihon / Symbol-Parser

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Small class to parse debug info from PEs, download their respective PDBs from the Microsoft Public Symbol Server and calculate RVAs of functions

Updated Apr 6, 2020
C++

obliviateandsurrender / PDB-Reader

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This script aims at reading a given PDB file and generation dihedral angles from it.

pdb numpy protein-structure dihedral-angles pdb-files

Updated Sep 27, 2017
Python

normcyr / new-pdb-inspector

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Search for new PDB structures corresponding to a search term and deposited after a certain date.

biology pdb protein-structure biochemistry nmr-spectroscopy pdb-files xray-crystallography

Updated Aug 2, 2017
Python

obliviateandsurrender / ORF-finder-Protien-Sequence-Generator

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This script allows us to generate ORF for a given Protein Sequence.

protein-structure protein-sequences fasta-sequences pdb-files

Updated May 2, 2017
Python

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