tyang816/SES-Adapter

Structure-aware adapter fine-tuning PLMs, with high training speed and impressive performance.

Language: Python - Size: 107 MB - Last synced: about 2 hours ago - Pushed: about 3 hours ago - Stars: 7 - Forks: 0

kiharalab/DiffModeler

DiffModeler: a diffusion model based protein complex structure modeling tool.

Language: Python - Size: 13 MB - Last synced: about 2 hours ago - Pushed: about 3 hours ago - Stars: 13 - Forks: 1

project-gemmi/gemmi

macromolecular crystallography library and utilities

Language: C++ - Size: 8.57 MB - Last synced: about 1 hour ago - Pushed: about 12 hours ago - Stars: 198 - Forks: 38

colbyford/SARS-CoV-2_BA.2.86_Spike-RBD_Predictions

Predicting Antibody and ACE2 Affinity for SARS-CoV-2 BA.2.86 with In Silico Protein Modeling and Docking

Language: Mermaid - Size: 152 MB - Last synced: about 14 hours ago - Pushed: about 15 hours ago - Stars: 1 - Forks: 0

westlake-repl/SaProt

Saprot: Protein Language Model with Structural Alphabet

Language: Python - Size: 2.49 MB - Last synced: about 20 hours ago - Pushed: about 21 hours ago - Stars: 220 - Forks: 19

mpavsic/sbio

Struktura proteinov [UL FKKT]

Language: TeX - Size: 810 MB - Last synced: about 4 hours ago - Pushed: about 22 hours ago - Stars: 0 - Forks: 0

Pawansit/StructureAnalyst

Get the Short Macromolecular level Summary for mmCIF file.

Language: Python - Size: 58.6 KB - Last synced: about 22 hours ago - Pushed: about 24 hours ago - Stars: 1 - Forks: 0

bowman-lab/enspara

Modeling molecular ensembles with scalable data structures and parallel computing

Language: Python - Size: 9.2 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 33 - Forks: 15

williamgilpin/pypdb

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

Language: Python - Size: 613 KB - Last synced: about 13 hours ago - Pushed: 1 day ago - Stars: 297 - Forks: 75

Dan-Burns/ChACRA

Reveal protein energy centers.

Language: Python - Size: 5.38 MB - Last synced: 1 day ago - Pushed: 1 day ago - Stars: 1 - Forks: 2

MooersLab/rstudiopymolpysnips

PyMOL snippet library is written in Python for use in RStudio via the R reticulate package and the PyMOL Python API.

Language: Vim Snippet - Size: 224 MB - Last synced: 1 day ago - Pushed: 2 days ago - Stars: 1 - Forks: 0

RosettaCommons/rosetta

The Rosetta Bio-macromolecule modeling package.

Language: C++ - Size: 1.72 GB - Last synced: about 19 hours ago - Pushed: 2 days ago - Stars: 65 - Forks: 42

bioinf-mcb/Metagenomic-DeepFRI

Pipeline for searching and aligning contact maps for proteins, then running DeepFri's GCN.

Language: Python - Size: 6.5 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 29 - Forks: 6

salilab/rmf

The library to support reading and writing of RMF files.

Language: C++ - Size: 36.2 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 7 - Forks: 0

biopython/biopython

Official git repository for Biopython (originally converted from CVS)

Language: Python - Size: 67.9 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 4,182 - Forks: 1,720

aqlaboratory/openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

Language: Python - Size: 15.3 MB - Last synced: 3 days ago - Pushed: 4 days ago - Stars: 2,420 - Forks: 442

BradyAJohnston/MolecularNodes

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

Language: Python - Size: 742 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 796 - Forks: 81

opendilab/awesome-AI-based-protein-design

A collection of research papers for AI-based protein design

Size: 543 KB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 186 - Forks: 12

diegozea/MIToS.jl

Mutual Information Tools for protein Sequence analysis in Julia

Language: Julia - Size: 48.6 MB - Last synced: 4 days ago - Pushed: 5 days ago - Stars: 64 - Forks: 18

tyang816/ProtSSN

Fusion of protein sequence and structural information, using denoising pre-training network for protein engineering (zero-shot).

Language: Python - Size: 28.4 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 17 - Forks: 0

salilab/imp

The Integrative Modeling Platform

Language: C++ - Size: 224 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 67 - Forks: 31

gph82/mdciao

mdciao: Analysis of Molecular Dynamics Simulations Using Residue Neighborhoods

Language: Python - Size: 70.2 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 29 - Forks: 4

althonos/mini3di

A NumPy port of the foldseek code for encoding protein structures to 3di.

Language: Python - Size: 360 KB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 12 - Forks: 1

y1zhou/arpeggia

Calculation of interatomic interactions in molecular structures

Language: Rust - Size: 84 KB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 0 - Forks: 0

hfswetton/PDBCor Fork of dzmitryashkinadze/PDBCor

Extraction of correlations from multistate PDB protein coordinates

Language: Python - Size: 11.7 MB - Last synced: 6 days ago - Pushed: 7 days ago - Stars: 0 - Forks: 0

steineggerlab/foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

Language: C - Size: 24.2 MB - Last synced: 3 days ago - Pushed: 8 days ago - Stars: 656 - Forks: 90

wells-wood-research/de-stress

DE-STRESS is a model evaluation pipeline that aims to make protein design more reliable and accessible.

Language: Elm - Size: 21.9 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 15 - Forks: 1

nf-core/proteinfold

Protein 3D structure prediction pipeline

Language: Nextflow - Size: 5.58 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 41 - Forks: 27

MooersLab/jupyterlabpymolpysnips

Python snippets for PyMOL to be run in Jupyterlab via the jupyterlab-snippets-multimenus extension.

Language: HTML - Size: 8.76 MB - Last synced: 8 days ago - Pushed: 8 days ago - Stars: 19 - Forks: 5

MooersLab/colabpymolpysnips

Library of PyMOL Python snippets for Google Colab.

Language: Jupyter Notebook - Size: 2.41 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 3 - Forks: 7

zaixizhang/PocketGen

Implementation of PocketGen: Generating Full-Atom Ligand-Binding Protein Pockets

Language: Python - Size: 15.6 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 42 - Forks: 5

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: 10 days ago - Pushed: 10 days ago - Stars: 32 - Forks: 7

Jhsmit/PyHDX

Derive ΔG for single residues from HDX-MS data

Language: Python - Size: 45.9 MB - Last synced: 10 days ago - Pushed: 10 days ago - Stars: 28 - Forks: 11

dominiquefastus/AlphaFoldPipeline-ALFOtask

In this research project a standardised AlphaFold 2-based molecular replacement strategy is developed and implemented in an existing biomolecule structure solution pipeline at MAX IV Laboratory. It can be run on high performance clusters similar to the LUNARC (https://www.lunarc.lu.se/). A standalone and implemented version of the pipeline exists.

Language: Python - Size: 140 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 0 - Forks: 0

BioPandas/biopandas

Working with molecular structures in pandas DataFrames

Language: Python - Size: 21.9 MB - Last synced: 1 day ago - Pushed: 11 days ago - Stars: 685 - Forks: 116

a-r-j/graphein

Protein Graph Library

Language: Jupyter Notebook - Size: 87.8 MB - Last synced: 3 days ago - Pushed: 13 days ago - Stars: 987 - Forks: 122

kliment-olechnovic/ftdmp

FTDMP is a software system for running docking experiments and scoring/ranking multimeric models.

Language: C++ - Size: 96.2 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 8 - Forks: 1

kliment-olechnovic/voronota

Voronota is a software tool for analyzing three-dimensional structures of biological macromolecules using the Voronoi diagram of atomic balls.

Language: C++ - Size: 431 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 21 - Forks: 3

Bio2Byte/Scop3P-notebooks

Jupyter notebook examples of SCOP3P REST API services

Language: Jupyter Notebook - Size: 726 KB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 1 - Forks: 1

greener-group/progres

Fast protein structure searching or your money back

Language: Python - Size: 217 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 67 - Forks: 3

gauravcodepro/domain-analyzer

This repository contains a datascience based faster implementation of the domain predictions from the interpro scan and it will give you a complete domains information, coordinates and other associative information. I used a mapping dataframe approach to make it faster rather than looping it over and over.

Language: Python - Size: 64.5 KB - Last synced: 9 days ago - Pushed: 15 days ago - Stars: 0 - Forks: 0

gdocking/gdock

Protein-Protein Docking using Genetic Algorithm

Language: Python - Size: 6.65 MB - Last synced: 15 days ago - Pushed: 17 days ago - Stars: 14 - Forks: 2

hshadman/2d_conformational_landscape_map

Use PyConforMap to generate a simple scatter plot to map conformational landscapes of intrinsically disordered proteins, and quantify conformational diversity.

Language: Jupyter Notebook - Size: 23.4 MB - Last synced: 17 days ago - Pushed: 17 days ago - Stars: 0 - Forks: 0

tawssie/ZMPY3D_TF

Python implementation of 3D Zernike moments with Tensorflow

Language: Python - Size: 15.2 MB - Last synced: 17 days ago - Pushed: 18 days ago - Stars: 0 - Forks: 0

tawssie/ZMPY3D_CP

Python implementation of 3D Zernike moments with CuPy

Language: Python - Size: 15.2 MB - Last synced: 17 days ago - Pushed: 18 days ago - Stars: 0 - Forks: 0

tawssie/ZMPY3D

Python implementation of 3D Zernike moments with NumPy

Language: Python - Size: 15.4 MB - Last synced: 17 days ago - Pushed: 18 days ago - Stars: 0 - Forks: 0

biojava/biojava

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

Language: Java - Size: 48.1 MB - Last synced: 21 days ago - Pushed: 21 days ago - Stars: 574 - Forks: 376

mims-harvard/SPECTRA

Spectral Framework For AI Model Evaluation

Language: Roff - Size: 70 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 13 - Forks: 1

mckeownish/Wiggle

Python library for implementing geometrical representations of curves.

Language: Python - Size: 246 KB - Last synced: 25 days ago - Pushed: 25 days ago - Stars: 0 - Forks: 0

scipion-chem/scipion-chem

Base Scipion plugin defining objects and protocols for CHEMoinformatics

Language: Python - Size: 1.48 MB - Last synced: 25 days ago - Pushed: 25 days ago - Stars: 6 - Forks: 1

samberry19/bioviper

Enhancements to Biopython for working with biological data

Language: Jupyter Notebook - Size: 9.92 MB - Last synced: 22 days ago - Pushed: 26 days ago - Stars: 6 - Forks: 1

proteinevolution/Toolkit

The MPI Bioinformatics Toolkit

Language: Scala - Size: 47.7 MB - Last synced: 26 days ago - Pushed: 26 days ago - Stars: 60 - Forks: 14

a-r-j/ProteinWorkshop

Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)

Language: Python - Size: 21.4 MB - Last synced: 2 days ago - Pushed: 27 days ago - Stars: 153 - Forks: 13

lightdock/lightdock-rust

A Rust implementation of the LightDock macromolecular docking software

Language: Rust - Size: 10.5 MB - Last synced: 27 days ago - Pushed: 28 days ago - Stars: 23 - Forks: 5

althonos/pyjess

Cython bindings and Python interface to Jess, a 3D template matching software for protein structures.

Language: Cython - Size: 185 KB - Last synced: 28 days ago - Pushed: 29 days ago - Stars: 1 - Forks: 0

gappeah/Nucleic-Acid-Converter-and-Secondary-Structure-Predictor

Designed to convert DNA or RNA sequences into amino acids and predict their secondary structure based on the amino acid sequence.

Language: Python - Size: 4.88 KB - Last synced: 30 days ago - Pushed: 30 days ago - Stars: 0 - Forks: 0

PDB-REDO/libcifpp

Library containing code to manipulate mmCIF and PDB files

Language: C++ - Size: 10.5 MB - Last synced: 29 days ago - Pushed: 30 days ago - Stars: 27 - Forks: 9

psipred/hspred

Protein-protein interaction hotspot predictor

Language: Perl - Size: 366 KB - Last synced: 30 days ago - Pushed: 30 days ago - Stars: 1 - Forks: 0

djmaity/md-davis

MD DaVis: A python package to analyze molecular dynamics trajectories of proteins

Language: Python - Size: 60.9 MB - Last synced: 13 days ago - Pushed: about 1 month ago - Stars: 11 - Forks: 4

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: 3 days ago - Pushed: about 1 month ago - Stars: 5 - Forks: 1

rdk/p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

Language: Groovy - Size: 365 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 216 - Forks: 32

JuliaMolSim/Molly.jl

Molecular simulation in Julia

Language: Julia - Size: 81.5 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 361 - Forks: 51

kiharalab/DeepMainMast

DeepMainmast

Language: C - Size: 79.6 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 8 - Forks: 1

flatironinstitute/deepblast

Neural Networks for Protein Sequence Alignment

Language: Python - Size: 56.7 MB - Last synced: 24 days ago - Pushed: about 1 month ago - Stars: 96 - Forks: 16

ugSUBMARINE/shortest-path

Find shortest path between selected residues in a protein structure

Language: Python - Size: 1.23 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

ugSUBMARINE/motif-search

Searching for motifs / side chain constellations in a proteins structure

Language: Python - Size: 620 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 1

BioJulia/BioStructures.jl

A Julia package to read, write and manipulate macromolecular structures (particularly proteins)

Language: Julia - Size: 4.79 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 85 - Forks: 22

alxdrcirilo/ramachandraw

Ramachandran plotting tool

Language: Python - Size: 770 KB - Last synced: 12 days ago - Pushed: about 1 month ago - Stars: 18 - Forks: 10

pswanson1/PPM

PPM.Mk.I.Beta

Language: Python - Size: 56.6 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 0 - Forks: 0

RachelAlcraft/prometry

A library to calculate geometric parameters of protein structures and perform criteria search

Language: Python - Size: 741 KB - Last synced: 12 days ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

KargKarg/prediction_structure_secondaire

Language: Jupyter Notebook - Size: 10.2 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

pharmai/plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

Language: Python - Size: 8.91 MB - Last synced: 20 days ago - Pushed: about 2 months ago - Stars: 400 - Forks: 97

comp-medchem/LigExtract

Performs large-scale ligand identification, curation and extraction from human structures in the Protein Data Bank.

Language: Python - Size: 1.84 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 1

kantonopoulos/ProteinSS-Prediction-Keras

Enhancing protein secondary structure prediction using neural networks in Python with Keras, implemented as part of bioinformatics course.

Language: Jupyter Notebook - Size: 10.3 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

omarperacha/ps4-dataset

The largest open-source dataset for Protein Single Sequence Secondary Structure prediction.

Language: Python - Size: 4.4 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 7 - Forks: 0

salilab/pmi

Python Modeling Interface

Language: Python - Size: 80.2 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 11 - Forks: 11

ugSUBMARINE/psatm

Create pseudoatoms at the centroid of the catalytic atoms of a residue

Language: Rust - Size: 719 KB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

jonathanking/sidechainnet

An all-atom protein structure dataset for machine learning.

Language: Python - Size: 55.3 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 296 - Forks: 35

FrankPolak/Structural_Bioinformatics

Protein Structure Prediction using Bioinformatics

Language: Python - Size: 697 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

algbio/emerald

EMERALD calculates safety-windows by exploring the suboptimal alignment space

Language: C++ - Size: 1.43 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 15 - Forks: 0

lcrawlab/SINATRA-Pro

Topological data analytic approach for discovering biophysical signatures in protein dynamics

Language: Python - Size: 34.3 MB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 4 - Forks: 1

strumenti-formali-per-la-bioinformatica/contrastive-3d-protein-prediction Fork of angelonazzaro/contrastive-3d-protein-prediction

[a.a. 23/24] A. Nazzaro, L. Costante

Language: Python - Size: 57.1 MB - Last synced: 24 days ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

angelonazzaro/contrastive-3d-protein-prediction

A contrastive approach for 3d protein prediction.

Language: Python - Size: 57.1 MB - Last synced: 24 days ago - Pushed: 2 months ago - Stars: 1 - Forks: 2

KarchinLab/HotMAPS_2016

Detects hotspot regions for somatic mutations in 3D protein structures

Language: Python - Size: 113 KB - Last synced: about 2 months ago - Pushed: 2 months ago - Stars: 20 - Forks: 15

chao1224/ProteinDT

Language: Python - Size: 19.3 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 14 - Forks: 0

jordantwells42/structural-replacement

A suite of scripts for performing structural replacement i.e. removing a structural feature of a protein and replacing it with a ligand, utilizing PyRosetta.

Language: Python - Size: 652 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 2 - Forks: 1

huiwenke/MineProt

Stand-alone server for structural proteome curation

Language: PHP - Size: 5.95 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 5 - Forks: 0

ahabegger/CA-2-HCOMB

CA-2-HCOMB is a tool for simplifying single-chain protein structures from PDB files into manageable models like various honeycombs, retaining essential information for in-depth computations. It's efficient for large datasets and machine learning, and user-friendly for research and education.

Language: Python - Size: 2.12 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

sarisabban/MiraMar

De novo cyclic protein polypeptide design using reinforcement learning.

Language: Python - Size: 2.26 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

salilab/cryptosite-web

Web server for prediction of cryptic binding sites

Language: Python - Size: 92.8 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

salilab/modloop

Web server for automated modeling of loops in protein structures

Language: Python - Size: 601 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 5 - Forks: 2

chaconlab/korpm

Predicting the effect of mutations on protein stability using a simple orientational potential.

Language: C++ - Size: 65.5 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 11 - Forks: 4

ahabegger/HCOMB-2-CA

Lattice2Backbone is a software tool that converts lattice representations of protein structures into detailed, carbon alpha-only backbone structures, bridging the gap between simplified models and comprehensive biological analysis in structural biology and bioinformatics.

Language: Python - Size: 32.2 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

Degiacomi-Lab/molearn

protein conformational spaces meet machine learning

Language: Python - Size: 174 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 38 - Forks: 10

biojava/biojava-tutorial

:book::books:An introductory tutorial for BioJava

Language: Python - Size: 5.01 MB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 114 - Forks: 41

hpcaitech/FastFold

Optimizing AlphaFold Training and Inference on GPU Clusters

Language: Python - Size: 1.26 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 531 - Forks: 78

suraj5424/Protein-sequence-analysis

This notebook does the analysis of a protein sequence dataset in FASTA format. It addresses challenges in data import, alignment, embedding, and classification using bioinformatics tools and machine learning techniques. The solution provides a systematic approach to extract insights from structured data, crucial for bioinformatics research.

Language: Jupyter Notebook - Size: 1.23 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

salilab/allosmod-lib

Protocol to model with allostery

Language: Python - Size: 555 KB - Last synced: about 2 months ago - Pushed: 3 months ago - Stars: 4 - Forks: 0

DeepGraphLearning/esm-s

Structure-Informed Protein Language Model

Language: Python - Size: 928 KB - Last synced: 11 days ago - Pushed: 3 months ago - Stars: 23 - Forks: 3

adaptyvbio/ProteinFlow

Versatile computational pipeline for processing protein structure data for deep learning applications.

Language: Python - Size: 59.2 MB - Last synced: 8 days ago - Pushed: 3 months ago - Stars: 171 - Forks: 8