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1,092 search results found

Feature Viewer ⭐ 100

Library to visualize protein sequence features in javascript using D3 - From SIB CALIPHO group; neXtProt project

Protein-Level ASSembler (PLASS): sensitive and precise protein assembler

Ifeature ⭐ 99

iFeature is a comprehensive Python-based toolkit for generating various numerical feature representation schemes from protein or peptide sequences. iFeature is capable of calculating and extracting a wide spectrum of 18 major sequence encoding schemes that encompass 53 different types of feature descriptors. Furthermore, iFeature also integrates five kinds of frequently used feature clustering algorithms, four feature selection algorithms and three dimensionality reduction algorithms.

Ontoprotein ⭐ 98

Code and datasets for the ICLR2022 paper "OntoProtein: Protein Pretraining With Gene Ontology Embedding"

Bioblender ⭐ 98

AddOn for Blender to do molecular work

Chatdrug ⭐ 96

LLM for Drug Editing, ICLR 2024

Thermonet ⭐ 95

ThermoNet is a computational method for quantitative prediction of the impact of single-point mutations on protein thermodynamic stability. The core algorithm of ThermoNet is an ensemble of deep 3D convolutional neural networks.

Git repository for FASTA36 sequence comparison software

Proteinworkshop ⭐ 93

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

Proteinsecondarystructure Cnn ⭐ 93

Protein Secondary Structure predictor using Convolutional Neural Networks

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

Transvar ⭐ 91

TransVar - multiway annotator for precision medicine

Encoding/decoding library for Protobuf with schema-versioning and runtime-decoding capabilities.

Lasagne4bio ⭐ 88

Jax Unirep ⭐ 87

Reimplementation of the UniRep protein featurization model.

netZooR is a network biology package implemented in R.

Inference of couplings in proteins and RNAs from sequence variation

Raptorx 3dmodeling ⭐ 81

Note that current version does not include search of very large metagenome data. For some proteins, metagenome data is important. We will update this as soon as possible.

Protein Ebm ⭐ 81

Energy-based models for atomic-resolution protein conformations

Equidock_public ⭐ 81

EquiDock: geometric deep learning for fast rigid 3D protein-protein docking

Metamorpheus ⭐ 81

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities

Kaggle_human_protein_baseline ⭐ 81

Human Protein Atlas Image Classification baseline:0.456

Cpi_prediction ⭐ 80

This is a code for compound-protein interaction (CPI) prediction based on a graph neural network (GNN) for compounds and a convolutional neural network (CNN) for proteins.

Deepblast ⭐ 80

Neural Networks for Protein Sequence Alignment

Deepaffinity ⭐ 80

Protein-compound affinity prediction through unified RNN-CNN

Omnipathr ⭐ 80

R client for the OmniPath web service

Singlecellseq ⭐ 79

Batch effects and the effective design of single-cell gene expression studies

🧬 An R package for visualizing molecular data in 3D

A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence

PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.

Biostructures.jl ⭐ 77

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

Predict the binding affinity of protein-protein complexes from structural data

Protein Science ⭐ 76

A collection of useful tutorials for Protein Science

Haddock3 ⭐ 76

Official repo of the modular BioExcel version of HADDOCK

Cblaster ⭐ 75

Find clustered hits from a BLAST search

Geom3D: Geometric Modeling on 3D Structures, NeurIPS 2023

DockQ is a single continuous quality measure for protein docked models based on the CAPRI evaluation protocol

A new approach for representing biological sequences

Fm Index ⭐ 71

FM-Index full-text index implementation using RRR Wavelet trees (libcds) and fast suffix sorting (libdivsufsort) including experimental results.

Transformercpi ⭐ 71

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524

Peptides ⭐ 71

An R package to calculate indices and theoretical physicochemical properties of peptides and protein sequences.

Opencadd ⭐ 70

A Python library for structural cheminformatics

Multiscalearrays.jl ⭐ 69

A framework for developing multi-scale arrays for use in scientific machine learning (SciML) simulations

A Python-based Effective Feature Generation Tool from DNA, RNA, and Protein Sequences

2019 Ncov ⭐ 68

Efforts towards proposing a potentially highly active molecule against a target protein of the 2019 Novel Coronavirus

Genome mapping and spliced alignment of cDNA or amino acid sequences

Pdbtools ⭐ 68

A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files

Deepnovo ⭐ 67

Protein Identification with Deep Learning

Dfast_core ⭐ 67

DDBJ Fast Annotation and Submission Tool

Awesome Deep Learning 4 Life Sciences ⭐ 65

A collection of resources for Deep Learning in Python for Life Sciences (with focus on biotech and pharma).

Mitos.jl ⭐ 64

Mutual Information Tools for protein Sequence analysis in Julia

Mmtf Pyspark ⭐ 64

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

Genomes Pipeline ⭐ 63

MGnify genome analysis pipeline

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.

FEELnc : FlExible Extraction of LncRNA

PyGBe: Python, GPUs and Boundary elements for electrostatics

Coronavirus_structural_task_force ⭐ 60

Repository for the molecular structures related with Corona virusses and their re-processing

Msgfplus ⭐ 60

MS-GF+ (aka MSGF+ or MSGFPlus) performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database.

Phylocsf ⭐ 60

Phylogenetic analysis of multi-species genome sequence alignments to identify conserved protein-coding regions

Equifold ⭐ 59

Official code repository for EquiFold

Python Graph Clustering ⭐ 59

A collection of Python scripts that implement various graph clustering algorithms, specifically for identifying protein complexes from protein-protein interaction networks.

The Databases For Drug Discovery ⭐ 59

The Databases for Drug Discovery (DDD)

Tesorter ⭐ 59

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes

Code associated with "Biophysical prediction of protein-peptide interactions and signaling networks using machine learning."

The Fluorescent Protein Database

High throughput protein function annotation with Human Readable Description (HRDs) and Gene Ontology (GO) Terms.

Udsmprot ⭐ 58

Protein sequence classification with self-supervised pretraining

Cytoself ⭐ 58

Self-supervised models for encoding protein localization patterns from microscopy images

Protein Residue-Residue Contacts from Correlated Mutations predicted quickly and accurately.

Getcontacts ⭐ 56

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation

This is the repository for PIPR. This repository contains the source code and links to some datasets used in the ISMB/ECCB-2019 paper "Multifaceted Protein-Protein Interaction Prediction Based on Siamese Residual RCNN".

Vscoding Sequence ⭐ 56

VSCode Extension for interactively visualising protein structure data in the editor

Crisprcasfinder ⭐ 54

A Perl script allowing to identify CRISPR arrays and associated Cas proteins from DNA sequences

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

Awesome Structural Bioinformatics ⭐ 54

Structural Bioinformatics is awesome. Throw your textbook in the garbage, light the garbage can on fire, and blend the ashes into your cold brew almond milk latte and read this.

A tool to identify CLIP-seq peaks

Protein Interaction Network ⭐ 53

Computes a molecular graph for protein structures.

Deepchem Gui ⭐ 53

A simple web GUI for DeepChem

Genomegtftools ⭐ 52

convert various features into a GFF-like file for use in genome browsers

A Deep-learning based dOcking decoy eValuation mEthod

Gym Lattice ⭐ 52

An HP 2D Lattice Environment with a Gym-like API for the Protein Folding Problem

Raptorx Contact ⭐ 52

Deep residual neural network for protein contact/distance prediction developed by Xu group

Genotify ⭐ 51

A minimal desktop app for easy and convenient gene annotation.

De novo protein structure prediction using iteratively predicted structural constraints

Cath Tools ⭐ 51

Protein structure comparison tools such as SSAP and SNAP

Bioinformatics utilities.

Picotti lab data analysis package.

Protein Alignment and Detection Interface

🧬 Toolkit for generating various numerical features of protein sequences

Cite Seq Count ⭐ 50

A tool that allows to get UMI counts from a single cell protein assay

A package to annotate protein sequences

Factored Attention ⭐ 50

This repository contains code for reproducing results in our paper Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention

Uniprotr ⭐ 49

Retrieving Information of Proteins from Uniprot

Protein Design Tutorials ⭐ 49

Tutorials, cheat sheets, and other resources for computational methods for protein design.

retrieve protein sequence identifiers and metadata from http://uniprot.org

D Script ⭐ 49

A structure-aware interpretable deep learning model for sequence-based prediction of protein-protein interactions

Nlp4sciencepapers ⭐ 49

Must-read papers on NLP for science.

Carnival ⭐ 48

CAusal Reasoning for Network Identification with integer VALue programming in R

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