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protein folding model using only general-purpose transformer layers, scaled

protein (RBP) binding motifs. RBPBench can be used for a variety

A seamless interface to the MEME Suite family of tools

Predicts transcription factor binding sites in up to 316 vertebrate

Protein Data Bank structures into 3D-printable models. Each polymer

Local Python sequence utilities for nucleotide composition, DNA and RNA

Local Windows-friendly R Shiny application for RNA-seq differential

protein structures. Membrane Visual QC provides planar membrane-relative geometry

AESTETIK is a deep learning model that jointly integrates spatial

Provides a comprehensive suite of functions to design and annotate

SpaceTrooper performs Quality Control analysis using data driven GLM models

Curated collection of agent skills for scientific research (InternScience, 493

protein language models into the R environment. Provides unified interfaces

protein engineering, and single-cell omics analysis (PharMolix & Tsinghua

Curated, multilingual library of 182 installable AI agent skills for

protein-language-model-informed token space; enables zero-shot cell

Long-context generative genomic foundation model using 6-mer tokenization

LLM papers for scientific discovery

protein target sequences. The mirnaprotpred package provides two core modules

Protein Language Models (PLMs). It uses trainable subnetworks to isolate

Cross-platform system optimizations for accelerating AlphaFold3 training with 1.73

CAPHEINE is a comprehensive computational workflow that automates exploratory evolutionary

Learning the language of protein-protein interactions

protein structure determination from electron density with high accuracy (3DEM/EMBL

proteins via backpropagation through compositional design constraints parameterized by structure

Interactive R package with an intuitive Shiny-based graphical interface

First fully open-source model achieving AlphaFold3-level accuracy with

CGAS is an automated Python-based pipeline providing a comprehensive

protein engineering. It orchestrates a unified ecosystem of specialized tools

gMISpy is a Python package designed to compute genetic Minimal

bifidoAnnotator is a bioinformatics tool designed for fine-grained annotation

A tool that enables in silico identification, integration, and modeling

protein-DNA binding preferences. It accepts various data types (ChIP

protein-protein interactions. The output would facilitate non-specific background

Tool to build force field input files for molecular simulation

protein antigens for subunit vaccine design against multidrug-resistant pathogens

protein fitness prediction and design, aggregating 200+ deep mutational scanning

protein conformational ensembles, covering both experimental PDB states and molecular

Create, handle, validate, visualize and convert networks in the Cytoscape

protein-coding genes, followed by enrichment analysis. Results can be visualized

maeparser is a parser for Schrodinger Maestro files.

protein language model using 3D structural vocabulary (Foldseek) for joint

protein language model translating between protein sequence and structure, finetuned

methods for predicting Enzyme Commission (EC) numbers from protein sequences.

protein schematics from Uniprot API output. From the JSON returned

protein sequence design over evolutionary-scale databases, supporting unconditional generation

protein-ligand complex structures with dynamic receptor conformational flexibility, enabling

Scanning (DMS) scores across protein domains, aiding systematic variant effect prediction.

This package provides functions for the analysis of data generated