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Generate new small molecules intended to bind a target protein with Boltz. The workflow covers cost estimation, job submission, result downloads, and ranking candidates by binding confidence or a score for improving promising molecules.
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Estimate small molecule solubility, permeability, and lipophilicity with Boltz using SMILES, a text notation for molecular structures. Process individual molecules or lists, review costs before submission, and receive results mapped to each input.
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Read, analyze, modify, and visualize molecular structures with RDKit in Python. Calculate molecular properties, search for similar structures or specific structural patterns, apply reaction rules, and generate 2D or 3D coordinates with detailed control over processing.
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Use PyTDC to discover therapeutic machine-learning datasets, create task-appropriate training and test splits, and evaluate predictions against curated benchmarks. Also score selected molecules with supported scoring functions, with explicit download plans and bounded outputs.
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Turn small-molecule structures into numerical features for similarity searches and models that predict activity or properties. Using Molfeat, the skill covers representation choices, invalid inputs, alignment with experimental labels, and saving feature-generation settings for reuse.
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Query the ChEMBL API for molecules, biological targets, activity records, and mechanisms of action. Search by text or look up an identifier, then receive concise summaries or JSON output when machine-readable results are needed.
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Author TOML-based Formula workflow templates that become Protomolecules and active Molecules in Gas Town's durable workflow system.
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The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules. It efficiently implements the machine learning model based on vectorization of nucleotide sequences and the random forest classification algorithm. The ORFhunteR package consists of a set of functions written in the R language in conjunction with C++. The efficiency of the package was confirmed by the examples of the analysis of RNA molecules fr
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MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells. The repertoire of antigens presented in a given genetic background largely depends on the sequence of the encoded MHC molecules, and thus, in humans, on the highly variable HLA (human leukocyte antigen) genes of the hyperpolymorphic HLA locus. More than 28,000 different HLA alleles have been reported, with significant differences in allele frequencies between human populations worldwide
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Cheminformatics toolkit catalog for small molecules. Covers RDKit/OpenChemLib calculations, descriptors, fingerprints, similarity/substructure search, R-group, MMP, scaffold tree, chemical space, MPO, reactions, and ADMET predictions. Open this skill when the user asks about computing molecular properties, comparing/searching molecules, or predicting ADMET/tox.
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Performs retrosynthetic planning using AiZynthFinder (MCTS, template-based), Chemformer (template-free transformer), ASKCOS, and emerging RetroSynFormer with explicit handling of route scoring, building-block availability (eMolecules, Enamine, Mcule), forward prediction validation (Molecular Transformer), and disconnection-aware multi-objective search (MO-MCTS). Use when assessing synthetic feasibility of generated or selected molecules, planning multi-step syntheses, building synthesis-aware design pipelines, or screening libraries for retro-route feasibility.
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Performs retrosynthetic planning using AiZynthFinder (MCTS, template-based), Chemformer (template-free transformer), ASKCOS, and emerging RetroSynFormer with explicit handling of route scoring, building-block availability (eMolecules, Enamine, Mcule), forward prediction validation (Molecular Transformer), and disconnection-aware multi-objective search (MO-MCTS). Use when assessing synthetic feasibility of generated or selected molecules, planning multi-step syntheses, building synthesis-aware design pipelines, or screening libraries for retro-route feasibility.
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Performs retrosynthetic planning using AiZynthFinder (MCTS, template-based), Chemformer (template-free transformer), ASKCOS, and emerging RetroSynFormer with explicit handling of route scoring, building-block availability (eMolecules, Enamine, Mcule), forward prediction validation (Molecular Transformer), and disconnection-aware multi-objective search (MO-MCTS). Use when assessing synthetic feasibility of generated or selected molecules, planning multi-step syntheses, building synthesis-aware design pipelines, or screening libraries for retro-route feasibility.
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Generate candidate positions and orientations for small molecules binding to proteins with DiffDock and DiffDock-L. Prepare single or batch docking runs, organize predicted poses by model confidence, and review validation needs without treating confidence as binding affinity.
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Plan or run targeted DNA panel analysis using UMIs, barcodes that identify DNA molecules. Organize consensus reads, coverage checks, and low-frequency variant results with molecular support, filtering reasons, and explicit quality limitations.
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Retrieve concise summaries from Reactome about biological pathways, events, participating molecules, and diagram-related data. Look up specific identifiers, search for relevant entries, or find pathways associated with an entity, and save the full response when needed.
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Screen supplied proteins, peptides, antibodies, or nanobodies against a target with Boltz. Prepares inputs, obtains a cost estimate for approval, downloads results, and ranks candidates by binding confidence, a score for predicted binding reliability.
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Generate new protein, peptide, antibody, or nanobody candidates that bind a chosen target using Boltz. The workflow covers target exploration, design setup, cost estimates, job submission, result downloads, and ranking by predicted binding confidence.
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Predict three-dimensional structures of complexes containing proteins, RNA, DNA, and small molecules with Chai-1. Compare candidate structures using confidence scores and clash indicators, or run repeated predictions from Python to evaluate designed binders.
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Use Boltz-2 to predict structures of complexes containing proteins, DNA, RNA, and small molecules. Obtain structure files and confidence scores to assess designed binders, with optional predictions of binding strength between a protein and a small molecule.
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Design protein sequences while accounting for bound small molecules, nucleic acids, or metals. Use LigandMPNN to redesign binding pockets or metal-coordinating sites, and export sequence files alongside PDB structures with the designed sequences applied.
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Graph-based drug discovery toolkit. Molecular property prediction (ADMET), protein modeling, knowledge graph reasoning, molecular generation, retrosynthesis, GNNs (GIN, GAT, SchNet), 40+ datasets, for PyTorch-based ML on molecules, proteins, and biomedical graphs.
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Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
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Generate novel drug-like molecules using the GenMol NIM microservice. Use for de novo generation, scaffold decoration, motif extension, lead optimization, SAFE notation, QED or LogP ranking, hosted NVIDIA API calls, or local Docker deployment. GenMol takes SAFE notation in the smiles field, not ordinary SMILES.
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