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Molecular dynamics analysis

PyTorch framework for training neural network interatomic potentials with the

protein language-model features, orthology, curated knowledge, protein association networks

protein folding and interactions. It calculates polar interaction changes and analyzes

This tool estimates the completeness of KEGG pathway modules from

Local-first, open-source healthcare AI toolkit for clinical NLP

protein interaction networks, and scientific knowledge graph learning (23.7k+ stars

protein conformational changes and characterize ligand dissociation pathways. It enables

The primary goal of this ontology is to standardize the

StaphScope is an automated, locally-executable computational pipeline designed specifically

Trainable PyTorch reproduction of AlphaFold 3

AcinetoScope is an automated, comprehensive bioinformatics pipeline designed specifically for

JCVI is a versatile toolkit for comparative genomics analysis. It

protein-coding sequences from over 20,000 species, enabling cross

proteins, nucleic acids, and complexes, featuring a public web server

Convert AMBER forcefields from ANTECHAMBER to GROMACS format.

protein equilibrium conformations 100,000× faster than MD simulations, predicting

protein sequence variants. It is used to convey variants in clinical

Curated library of 550+ medical research agent skills spanning evidence

MetaTracer is a nucleotide alignment-based framework that analyzes complex

This model card provides an overview of the intended use

state-of-the-art protein language model trained on billions of protein sequences…

state-of-the-art protein language model trained on billions of protein sequences…

state-of-the-art protein language model trained on billions of protein sequences…

protein language model that has learned the rules of protein

protein language model that has learned the rules of protein

protein language model that has learned the rules of protein

protein structure prediction and design that defines a new frontier

protein structure prediction and design that defines a new frontier

protein identifiers (TXT, CSV, TSV, XLSX). It maps approved symbols

The Ontology of Immune Epitopes (ONTIE) is an effort to

# Geneformer Geneformer is a foundational transformer model pretrained on a

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

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

See the upstream model card for full details, training data

kTYPr is an in silico tool designed to map the

Predicts transcription factor binding sites in up to 316 vertebrate

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

A structural pharmacology workbench for cognition-related CNS targets, built

Local Python sequence utilities for nucleotide composition, DNA and RNA

protein, structure, and single-cell tasks with reproducible CLIs and pretrained

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

OmniTCR is a component-aware autoregressive foundation model for learning

PertMind is a biological language model built around a central

protein language model for the phosphotransferase superfamily (EC 2.7.-: protein

protein variant classifier that predicts whether a mutated protein sequence

protein sequences using ESM2 embeddings and a trained 1-Dimensional

protein embeddings where biological similarity maps to embedding proximity. Intended

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids