biotite-dev/biotite

A comprehensive library for computational molecular biology

Language: Python - Size: 180 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 785 - Forks: 110

jianglab/HI3D

Helical indexing using the cylindrical projection of a 3D density map

Language: Python - Size: 3.69 MB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 3 - Forks: 1

Pranavkhade/PACKMAN

Python package built around protein structure and dynamics. OpenBabel-inspired objects.

Language: Python - Size: 12.3 MB - Last synced at: 3 days ago - Pushed at: 10 months ago - Stars: 36 - Forks: 7

haddocking/haddocking.github.io

Webpage of the Bonvinlab @ Utrecht University and HADDOCK software

Language: HTML - Size: 893 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 13 - Forks: 20

BradyAJohnston/MolecularNodes

Toolbox for molecular animations in Blender, powered by Geometry Nodes.

Language: Python - Size: 862 MB - Last synced at: 1 day ago - Pushed at: 2 days ago - Stars: 1,006 - Forks: 98

salilab/imp

The Integrative Modeling Platform

Language: C++ - Size: 227 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 76 - Forks: 30

cgoliver/rnaglib

Deep learning datasets for RNA 3D and 2.5D structures.

Language: Python - Size: 24 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 31 - Forks: 4

Lucaslab-Berkeley/Leopard-EM

Two-Dimensional Template Matching implemented in Python

Language: Python - Size: 1.08 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 4 - Forks: 4

febos/SQUARNA-data

SQUARNA benchmark data

Language: Jupyter Notebook - Size: 105 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0

project-gemmi/gemmi

macromolecular crystallography library and utilities

Language: C++ - Size: 9.84 MB - Last synced at: 6 days ago - Pushed at: 11 days ago - Stars: 253 - Forks: 47

PDBeurope/InvestigationCIF

Documentation for the mmcif Investigation dictionary

Size: 75.2 KB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 0 - Forks: 0

DeepRank/deeprank2

An open-source deep learning framework for data mining of protein-protein interfaces or single-residue variants.

Language: Python - Size: 107 MB - Last synced at: 6 days ago - Pushed at: 4 months ago - Stars: 49 - Forks: 11

a-r-j/graphein

Protein Graph Library

Language: Jupyter Notebook - Size: 86.8 MB - Last synced at: 6 days ago - Pushed at: about 2 months ago - Stars: 1,084 - Forks: 134

MDAnalysis/mdahole2

An MDAKit implementing a Python interface for the HOLE program.

Language: Python - Size: 15.3 MB - Last synced at: 2 days ago - Pushed at: about 1 month ago - Stars: 7 - Forks: 3

febos/SQUARNA

RNA secondary structure prediction tool

Language: Jupyter Notebook - Size: 162 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 14 - Forks: 2

samirelanduk/ZincBindDB

The database and API backend for ZincBind - the database of zinc binding sites

Language: Python - Size: 8.07 MB - Last synced at: 7 days ago - Pushed at: 12 days ago - Stars: 16 - Forks: 1

CBBIO/protein-metamorphisms-is

Functional sequence annotation, metamorphism and multifunctionality research over proteins

Language: Python - Size: 16.2 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 4 - Forks: 1

freesasa/freesasa-python

FreeSASA Python Module

Language: Cython - Size: 101 KB - Last synced at: 4 days ago - Pushed at: over 1 year ago - Stars: 53 - Forks: 14

proteinevolution/Toolkit

The MPI Bioinformatics Toolkit

Language: Scala - Size: 47.8 MB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 65 - Forks: 15

edikedik/lXtractor

Library for analysing protein structures and sequences

Language: Python - Size: 3.89 MB - Last synced at: 4 days ago - Pushed at: 15 days ago - Stars: 1 - Forks: 0

mpavsic/sbio

Struktura proteinov [UL FKKT]

Language: TeX - Size: 832 MB - Last synced at: 7 days ago - Pushed at: 17 days ago - Stars: 0 - Forks: 0

pyDock/AlphaFold3-Conda-Install

Step-by-step guide to install and configure AlphaFold 3 using a Conda Python 3.11 environment. No system-wide installations required. ✅ Miniconda setup & dependencies ✅ Repository cloning & model setup ✅ Database configuration & execution script 🔹 Requirements: Linux, NVIDIA GPU (Ampere+), CUDA, ~700GB disk space.

Language: Shell - Size: 113 KB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 1 - Forks: 0

carlocamilloni/Structural-Bioinformatics

This repository includes the slides and the practicals for the course of Structural Bioinformatics of the MBB/QB degrees at the University of Milano, originally inspired by https://github.com/pb3lab/ibm3202

Language: Jupyter Notebook - Size: 324 MB - Last synced at: 11 days ago - Pushed at: 17 days ago - Stars: 61 - Forks: 12

haddocking/haddock-runner

Run large scale HADDOCK simulations using multiple input molecules in different scenarios

Language: Go - Size: 2 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 5 - Forks: 2

johnnytam100/awesome-protein-design

A curated list of awesome protein design research, software and resources.

Size: 29.3 KB - Last synced at: 5 days ago - Pushed at: almost 3 years ago - Stars: 14 - Forks: 1

gph82/mdciao

mdciao: Accessible Analysis and Visualization of Molecular Dynamics Simulation Data

Language: Python - Size: 76.8 MB - Last synced at: 8 days ago - Pushed at: 22 days ago - Stars: 32 - Forks: 5

rtviii/riboxyz

Language: HTML - Size: 892 MB - Last synced at: 1 day ago - Pushed at: 24 days ago - Stars: 0 - Forks: 0

molstar/VSCoding-Sequence

VSCode Extension for interactively visualising protein structure data in the editor

Language: TypeScript - Size: 99.5 MB - Last synced at: 15 days ago - Pushed at: 5 months ago - Stars: 104 - Forks: 10

meilerlab/vustruct

VUStruct analyses sets of Variants of Unknown Significance (VUSs) by contextualizing them in 3D protein structural space.

Language: Python - Size: 6.5 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 0 - Forks: 0

jianglab/map2seq

Identify the best protein sequence that explains a 3D density map

Language: Python - Size: 12.8 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 0 - Forks: 1

jonathanking/sidechainnet

An all-atom protein structure dataset for machine learning.

Language: Python - Size: 55.3 MB - Last synced at: 16 days ago - Pushed at: about 1 year ago - Stars: 349 - Forks: 37

PDBeurope/protein-cluster-conformers

Clusters protein chains based on CA distance difference

Language: Python - Size: 105 MB - Last synced at: 9 days ago - Pushed at: 3 months ago - Stars: 14 - Forks: 0

rribeiro-sci/SSBtoolkit

Simulation of pharmacodynamic models of drug-GPCR (class A) interactions.

Language: Python - Size: 12.8 MB - Last synced at: 27 days ago - Pushed at: 27 days ago - Stars: 1 - Forks: 1

keiran-rowell/Presentations

Group meeting presentations and academic talks

Size: 252 MB - Last synced at: 28 days ago - Pushed at: 28 days ago - Stars: 0 - Forks: 0

GiatrasKon/Algorithms-in-Structural-Bioinformatics-Assignments

Assignments from the 'Algorithms in Structural Bioinformatics' graduate course, exploring RNA folding, molecular conformational analysis, and protein structure comparison using Python and bioinformatics tools.

Language: Jupyter Notebook - Size: 6.61 MB - Last synced at: 20 days ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0

ostrokach/proteinsolver

Graph neural network for generating novel amino acid sequences that fold into proteins with predetermined topologies.

Language: Jupyter Notebook - Size: 271 MB - Last synced at: 14 days ago - Pushed at: about 4 years ago - Stars: 59 - Forks: 8

Dan-Burns/ChACRA

Reveal protein energy centers.

Language: Python - Size: 5.42 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 3 - Forks: 2

BioJulia/BioStructures.jl

A Julia package to read, write and manipulate macromolecular structures

Language: Julia - Size: 9.25 MB - Last synced at: 1 day ago - Pushed at: 7 days ago - Stars: 99 - Forks: 23

OWissett/freesasa-rs

A rust crate to interface with the freesasa library for protein surface area calculations

Language: Rust - Size: 1.24 MB - Last synced at: 19 days ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 1

haddocking/pdb-tools

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

Language: Python - Size: 952 KB - Last synced at: 27 days ago - Pushed at: 8 months ago - Stars: 400 - Forks: 113

salilab/pmi

Python Modeling Interface

Language: Python - Size: 79.9 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 13 - Forks: 11

lbcb-sci/RiNALMo

RiboNucleic Acid (RNA) Language Model

Language: Python - Size: 363 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 89 - Forks: 16

fazekaszs/loco_hd

The LoCoHD metric for protein-protein structure comparison

Language: Python - Size: 4.52 MB - Last synced at: 10 days ago - Pushed at: 4 months ago - Stars: 13 - Forks: 2

david-bogdan-r/ARTEM

RNA/DNA 3D structure alignment tool

Language: Python - Size: 10.5 MB - Last synced at: 26 days ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

amjjbonvin/haddocking.github.io Fork of haddocking/haddocking.github.io

Webpage of the HADDOCK group

Language: HTML - Size: 878 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

GKLabIPR/MicroED

MicroED data processing scripts and tutorials

Language: Python - Size: 66.4 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 1 - Forks: 0

lightdock/lightdock

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

Language: Python - Size: 93.3 MB - Last synced at: about 1 month ago - Pushed at: 4 months ago - Stars: 324 - Forks: 45

sarisabban/DeepPhase 📦

Protein Crystal Classification Using Machine Learning

Language: Python - Size: 522 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 0

ncbi/HYDROID

Python package for analyzing hydroxyl-radical footprinting experiments of DNA-protein complexes

Language: Python - Size: 46.3 MB - Last synced at: 11 days ago - Pushed at: almost 4 years ago - Stars: 9 - Forks: 12

JMB-Scripts/AR-Structural-Biology

Augmented Reality object for biochemistry

Language: HTML - Size: 350 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0

samirelanduk/atomium

Python macromolecular parsing (with .pdb/.cif/.mmtf parsing and production)

Language: Python - Size: 31.1 MB - Last synced at: 9 days ago - Pushed at: over 1 year ago - Stars: 105 - Forks: 19

isambard-uob/isambard

Intelligent System for Analysis, Model Building And Rational Design of biomolecules.

Language: Python - Size: 8.18 MB - Last synced at: 9 days ago - Pushed at: about 4 years ago - Stars: 24 - Forks: 7

xroi/HS-AFM-Simulation

A model of high speed atomic force microscopy, based on density maps from IMP's Nuclear Pore Complex Transport module.

Language: Jupyter Notebook - Size: 4.12 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 0

haddocking/haddock-restraints

Generate restraints to be used in HADDOCK

Language: Rust - Size: 2.15 MB - Last synced at: 17 days ago - Pushed at: 20 days ago - Stars: 5 - Forks: 2

phonchi/Computational-CryoEM

A curated list of awesome computational cryo-EM methods.

Language: Jupyter Notebook - Size: 11.6 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 112 - Forks: 12

Joseph-Ellaway/Ramachandran_Plotter

Program to plot a Ramachandran plot of all dihedral angles from a given PDB file. Background is empirically generated from the peptides in the Top8000 PDB data set.

Language: Jupyter Notebook - Size: 78.1 MB - Last synced at: 14 days ago - Pushed at: about 2 months ago - Stars: 11 - Forks: 4

a-r-j/CPDB

Cython implementation of PDB -> DataFrame parsing

Language: Cython - Size: 18.7 MB - Last synced at: 14 days ago - Pushed at: almost 2 years ago - Stars: 23 - Forks: 0

PSSalgado/salgado-lab

Source for the Salgado Lab site

Language: HTML - Size: 9.91 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

SerenaRosi/SerenaRosi

SerenaRosi's GitHub page

Size: 68.4 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 3 - Forks: 0

sami-chaaban/subflow

Pipeline for on-the-fly subtraction of filaments from cryo-EM micrographs.

Language: Python - Size: 2.73 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

joelb123/rafm Fork of unmtransinfo/rafm

Reliable AlphaFold Measures

Language: Python - Size: 1.53 MB - Last synced at: 4 days ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0

samirelanduk/pdbsearch

A library for searching for PDB codes by consuming the RCSB web services.

Language: Python - Size: 46.9 KB - Last synced at: 6 days ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 0

samuellimce/pdbx

A PDBx/mmCIF-format parser and extractor.

Size: 1.95 KB - Last synced at: about 2 months ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 1

FragmentScreen/fandanGO-aria

Client library for interacting with ARIA APIs for data deposition.

Language: Python - Size: 167 KB - Last synced at: 15 days ago - Pushed at: 4 months ago - Stars: 3 - Forks: 0

multimeric/mmcifix

Fixes mmCIF protein structure files

Language: Python - Size: 253 KB - Last synced at: 18 days ago - Pushed at: about 2 years ago - Stars: 3 - Forks: 1

hbhargava7/cryoem-data-simulation

Python3 tools for simulating cryoEM particle data.

Language: Jupyter Notebook - Size: 10.2 MB - Last synced at: 18 days ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 1

poloarol/awesome-computational-biochemistry

Papers and Tools that would guide your journey in Computational Biochemistry

Size: 18.6 KB - Last synced at: 11 days ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 0

jaumebonet/FunFolDesData

Rosetta FunFolDes – a general framework for the computational design of functional proteins.

Language: Scala - Size: 2.22 GB - Last synced at: 14 days ago - Pushed at: about 6 years ago - Stars: 4 - Forks: 10

bartongroup/ProteoFAV

Open-source framework for simple and fast integration of protein structure data with sequence annotations and genetic variation

Language: Python - Size: 18.4 MB - Last synced at: 5 days ago - Pushed at: about 1 year ago - Stars: 4 - Forks: 0

LBC-LNBio/SERD

SERD: Solvent-Exposed Residues Detection

Language: Python - Size: 170 MB - Last synced at: 8 days ago - Pushed at: 2 months ago - Stars: 5 - Forks: 1

samirelanduk/pdb2json

A lightweight web app for converting molecular structures to JSON over the web.

Language: Python - Size: 5.86 KB - Last synced at: 6 days ago - Pushed at: over 4 years ago - Stars: 5 - Forks: 0

luquelab/pyCapsid

Python package to extract quasi-rigid domains in protein shells and other macromolecular complexes.

Language: HTML - Size: 114 MB - Last synced at: 9 days ago - Pushed at: about 1 year ago - Stars: 6 - Forks: 1

cvigilv/ResidueFisher

Bioinformatics protocol that aims at mining information at the sequence and structure level of protein chain to detect possible evolutionary conserved residues.

Language: Python - Size: 33.3 MB - Last synced at: 6 days ago - Pushed at: almost 2 years ago - Stars: 6 - Forks: 1

sklumpe/SerialFIB

A Modular Platform for Streamlining Automated Cryo-FIB Workflows

Language: Python - Size: 27.6 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 23 - Forks: 9

haddocking/prodigy-cryst

Contacts-based classifier of biological and crystallographic interfaces

Language: Python - Size: 3.31 MB - Last synced at: about 1 month ago - Pushed at: 12 months ago - Stars: 8 - Forks: 4

wudangt/awesome-molecular-modeling-and-drug-discovery

A curated list of awesome Molecular Modeling And Drug Discovery 🔥

Size: 51.8 KB - Last synced at: 5 days ago - Pushed at: over 2 years ago - Stars: 11 - Forks: 0

widdowquinn/Teaching-IBioIC-Intro-to-Bioinformatics

Course materials for the IBioIC Introduction to Bioinformatics training course

Language: HTML - Size: 94.7 MB - Last synced at: 11 days ago - Pushed at: almost 8 years ago - Stars: 12 - Forks: 7

Sarah-Hesham-2022/Unity-Protein-Visualization

Protein Visualization using Unity and C# analysis on PDB Files.

Language: C# - Size: 229 KB - Last synced at: 1 day ago - Pushed at: about 2 years ago - Stars: 14 - Forks: 1

sethaxen/MRCFile.jl

Read and write files and manipulate data in the MRC2014 format

Language: Julia - Size: 10.9 MB - Last synced at: 6 days ago - Pushed at: 5 months ago - Stars: 18 - Forks: 4

rebelot/schrodinger_utils

Various integrations to the Schrodinger ecosystem. With major interest on analysis tools for Molecular Dynamics simulations run with Desmond.

Language: Python - Size: 451 KB - Last synced at: 17 days ago - Pushed at: 10 months ago - Stars: 19 - Forks: 7

MPI-Dortmund/pymissense

PyMissense creates the pathogenicity plot and modified pdb as shown in the AlphaMissense paper for custom proteins.

Language: Python - Size: 1.03 MB - Last synced at: 7 days ago - Pushed at: over 1 year ago - Stars: 23 - Forks: 0

KudryashevLab/TomoBEAR

TomoBEAR is a configurable and customizable modular pipeline for streamlined processing of cryo-electron tomographic data for subtomogram averaging.

Language: MATLAB - Size: 2.96 MB - Last synced at: 9 days ago - Pushed at: about 1 year ago - Stars: 28 - Forks: 6

jgreener64/Bio3DView.jl

A Julia package to view macromolecular structures in the REPL, in a Jupyter notebook/JupyterLab or in Pluto

Language: Julia - Size: 24.1 MB - Last synced at: 13 days ago - Pushed at: 5 months ago - Stars: 35 - Forks: 7

haddocking/haddock-tools

Set of useful HADDOCK utility scripts

Language: Python - Size: 244 KB - Last synced at: 19 days ago - Pushed at: 8 months ago - Stars: 51 - Forks: 19

chopralab/lemon

A framework for rapidly mining structural information from the Protein Data Bank

Language: C++ - Size: 7.62 MB - Last synced at: 9 days ago - Pushed at: almost 5 years ago - Stars: 53 - Forks: 12

cxhernandez/ipymol

Control PyMOL sessions via IPython

Language: Python - Size: 3.27 MB - Last synced at: 12 days ago - Pushed at: over 2 years ago - Stars: 58 - Forks: 19

SBRG/ssbio

A Python framework for structural systems biology

Language: Python - Size: 38.2 MB - Last synced at: 15 days ago - Pushed at: over 4 years ago - Stars: 107 - Forks: 28

Genentech/equifold

Official code repository for EquiFold: Protein Structure Prediction with a Novel Coarse-Grained Structure Representation

Language: Python - Size: 13.8 MB - Last synced at: 7 days ago - Pushed at: over 2 years ago - Stars: 120 - Forks: 17

CDCgov/app-squared Fork of nicolepaterson/APPSquared

Protein analysis pipeline for characterizing influenza antigenic drift

Language: Python - Size: 1.77 MB - Last synced at: 2 days ago - Pushed at: 2 months ago - Stars: 0 - Forks: 2

salilab/rmf

The library to support reading and writing of RMF files.

Language: C++ - Size: 36.2 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 8 - Forks: 0

rvhonorato/cealign

Implementation of the Combinatorial Extension (cealign) algorithm to align protein structures

Language: Rust - Size: 131 KB - Last synced at: 26 days ago - Pushed at: 9 months ago - Stars: 2 - Forks: 0

GiovanniMerici/Autodock-Vina

Simple pipeline to execute molecular docking experiments

Language: Jupyter Notebook - Size: 3.17 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

jianglab/procart

A Web app that plots a cartoon to illustrate the residue properties of amyloid proteins in the context of their atomic structures

Language: Python - Size: 2.33 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

salilab/cross_linking_tutorial

Introduction to working with cross-linking data using IMP

Language: Jupyter Notebook - Size: 5.32 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0

yamule/SurfStamp-public

3D Printer Compatible Molecular Surface Representation (Do not clone! Everything is in the release page!)

Size: 24.6 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 8 - Forks: 0

XuanVuNguyen/TMFinder

TMFinder: Locating transmembrane region of proteins

Language: Python - Size: 1.09 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

maiabennett/PIEMA-benchmark-analysis

An analysis aimed at providing a benchmark of the PIEMA tool for T cell receptor (TCR) structural similarity identification. This analysis also extends PIEMA through the implementation of multiple Logistic Regression classifiers incorporating sequence and structural features to make predictions on shared specificity between TCRs.

Language: R - Size: 1.18 GB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

MzamoTembe/autoencoder

An autoencoder designed for dimensionality reduction of a protein structure's feature space that describes the structural environment of an amino acid by looking at the relative relative positions, orientations and dihedral angles of neighbouring residues in Euclidean space.

Language: Python - Size: 18.4 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

GiatrasKon/PTEN-MolecularDynamics-DrugDesign

Comprehensive molecular dynamics simulations and drug design analysis for PTEN protein: workflows include protein dynamics, binding site detection, ligand screening, and filtering for therapeutic discovery.

Language: Jupyter Notebook - Size: 40.9 MB - Last synced at: 20 days ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

jianglab/ctfsimulation

A CTF Simulation Web App

Language: Python - Size: 3.14 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 10 - Forks: 2