Results for “protein-modeling”

Generate, predict, and embed protein sequences and structures using ESM3, ESMC, and ESMFold2 with local or cloud inference.

Conjunto abrangente de ferramentas para modelos de linguagem de proteínas, incluindo ESM3 (design multimodal generativo de proteínas em sequência, estrutura e função) e ESM C (embeddings e representações eficientes de proteínas). Use essa skill ao trabalhar com sequências de proteínas, estruturas ou predição de função; designing de proteínas inovadoras; geração de embeddings de proteínas; inverse folding; ou tarefas de engenharia de proteínas. Suporta tanto uso local de modelos quanto Forge API baseada em nuvem para inferência escalável.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use this skill when working with protein sequences, structures, or function prediction; designing novel proteins; generating protein embeddings; performing inverse folding; or conducting protein engineering tasks. Supports both local model usage and cloud-based Forge API for scalable inference.

Generates and analyzes protein sequences and structures using ESM3, ESMC, and ESMFold2, with support for local and cloud inference.

Generates and analyzes proteins using ESM3 and ESM C language models, covering sequence generation, structure prediction, inverse folding, embeddings, and function conditioning with local or cloud-based Forge API inference.

Trains, evaluates, exports, and runs inference for person re-identification models using TAO, learning discriminative embeddings for cross-camera matching.

Run ESM protein language models — ESM3 for generative multimodal protein design across sequence, structure, and function, and ESM C for efficient embeddings and representations — locally or via the cloud Forge API. Use when working with protein sequences, structures, or function prediction, designing novel proteins, generating protein embeddings, performing inverse folding, or doing protein-engineering tasks. Part of the AlterLab Academic Skills suite.

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

Applies physical principles to model biological systems, including protein folding, membrane transport, molecular forces, and neural signaling.

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.

Predict 3D binding poses of small molecule ligands to protein targets using diffusion-based molecular docking, supporting single complexes, batch processing, and virtual screening.

Bayesian modeling with PyMC. Build hierarchical models, MCMC (NUTS), variational inference, LOO/WAIC comparison, posterior checks, for probabilistic programming and inference.

Advanced Optics Modeling Skill

LoRA: Low-Rank Adaptation of Large Language Models

Analyze and engineer protein glycosylation by scanning sequences for N-glycosylation sequons, predicting O-glycosylation hotspots, and accessing curated glycoengineering tools for therapeutic antibody optimization and vaccine design.

Acoustics Based Modeling Skill

Botany Based Modeling Skill

Battle-tested PyTorch training recipes for all domains — LLMs, vision, diffusion, medical imaging, protein/drug discovery, spatial omics, genomics. Covers training loops, optimizer selection (AdamW, Muon), LR scheduling, mixed precision, debugging, and systematic experimentation. Use when training or fine-tuning neural networks, debugging loss spikes or OOM, choosing architectures, or optimizing GPU throughput.

Use when searching protein sequences against profile hidden Markov models (HMMs) such as Pfam or other HMM databases.

Use when searching one or more protein query sequences against a protein sequence database with HMMER's one-pass sequence-vs-sequence searcher.

Co-fold biomolecular complexes with Boltz-2, an open AlphaFold3-style model — predict protein + ligand (SMILES/CCD), protein + nucleic-acid, and multi-chain structures in one pass, with binding-affinity prediction. Use when folding a protein together with a small-molecule ligand, predicting a holo (ligand-bound) complex or its binding affinity, or co-folding protein–DNA/RNA assemblies. For protein-only or protein–protein folding without ligands prefer alterlab-alphafold; for antibody–antigen complexes prefer alterlab-chai; to dock a ligand into a FIXED receptor structure prefer alterlab-diffdock; to look up an existing structure prefer alterlab-pdb. Part of the AlterLab Academic Skills suite.

Applied Botany Modeling Skill

Train, evaluate, export, and run inference for Masked Auto-Encoder (MAE) models for self-supervised pretraining and fine-tuning of visual representations.

Train, evaluate, distill, quantize, export, and run inference for PyTorch-based TAO image classification models with support for multiple backbones.

Detect poisoned training data and backdoored models across the ML pipeline using statistical analysis, activation clustering, and spectral signatures.

Botany Modeling Expert Skill

Constraint-based metabolic modeling (COBRA). FBA, FVA, gene knockouts, flux sampling, SBML models, for systems biology and metabolic engineering analysis.

Turns model work into a production ML system with data contracts, reproducible training, quality gates, deployable artifacts, and monitoring.