Biology & Genomics

Run an end-to-end drug discovery pipeline with BioNeMo NIM microservices

Generate and analyze DNA sequences with the Evo 2 BioNeMo NIM

Generate drug-like molecules and optimize leads with the GenMol NIM

Add optional GPU steps to genomics pipelines with NVIDIA Parabricks

Add a cMIM decoder to a grover_base checkpoint and continue hybrid pretraining

Continue KERMT pretraining on your own SMILES corpus in a container

Extract per-molecule embeddings from KERMT checkpoints as NumPy files

Fine-tune a KERMT molecular encoder on your labeled CSV data in a container

Predict molecular properties from SMILES CSVs with a fine-tuned KERMT model

Check progress of detached KERMT training runs and read their logs

Pretrain a new KERMT molecular model from scratch on your SMILES corpus

Set up the KERMT environment with Docker, GPU checks and a smoke test

Generate and optimize small molecules in latent space with MolMIM NIM

Generate protein multiple sequence alignments with the ColabFold MSA-Search NIM

Run a protein structure prediction pipeline from sequence search to folding

Write and debug GPU-accelerated RDKit fingerprint and similarity code with nvMolKit

Predict monomer protein structures from sequences with the OpenFold2 NIM

Predict protein, ligand and nucleic acid complex structures with OpenFold3 NIM

Plan NVIDIA Parabricks pbrun commands and map CPU options to GPU equivalents

Design protein sequences for a backbone with ProteinMPNN inverse folding NIM

Co-design protein structures and sequences with the RFD4-Proteina NIM

Design protein backbones and binders with RFDiffusion NIM

Run KEGG pathway enrichment, drug-target and metabolic network analysis

Fetch AlphaFold structures by UniProt ID and read pLDDT confidence scores

Build AlphaGenome Atlas links for variants, loci and prediction views

Analyze how a genetic variant affects gene expression and chromatin with AlphaGenome

Score genetic variant impact with AlphaGenome AVI scores and saturation scans

Query ChEMBL for bioactive compounds, drug targets and IC50 data

Look up SNPs in dbSNP by rsID, VCF coordinates or HGVS strings

Search EMBL-EBI OLS for biomedical ontology terms and their hierarchies

Query ENCODE cCRE regulatory elements and ChIP-seq experiment files

Resolve Ensembl gene IDs, fetch sequences and run variant effect prediction

Find proteins structurally similar to your PDB or mmCIF file with Foldseek

Check variant allele frequencies and gene constraint scores in gnomAD

Pull GTEx tissue expression levels and eQTL variant data for genes

Get Human Protein Atlas protein expression and subcellular location data

Find protein domains, families and GO terms with InterPro annotations

Fetch JASPAR transcription factor binding matrices in MEME and TRANSFAC formats

Fetch protein and nucleotide sequences from NCBI by accession or gene

Find drug targets and disease links with Open Targets evidence data

Search and download experimental 3D structures from the Protein Data Bank

Align multiple protein sequences with Clustal Omega to check conservation

Find homologous protein sequences with MMseqs2 or BLAST searches

Render protein structures in PyMOL with alignments and distance measures

Map genes to Gene Ontology terms and explore GO hierarchies with QuickGO

Run Reactome pathway enrichment and map identifiers to pathways

Find protein interaction partners and enrichment with STRING scores

Fetch phyloP and phastCons conservation scores and TF binding sites from UCSC

Download UniBind transcription factor binding sites as BED or FASTA