OpenMM — high-performance molecular dynamics simulation toolkit with GPU acceleration via CUDA and OpenCL. Provides Python API for building custom simulations, force field support (AMBER, CHARMM, AMOE
Use with AI
Install the MCP server or CLI to instantly fetch OpenMM documentation:
Install command
claude mcp add biocontext7 -- npx @biocontext7/mcpOr share this page: biocontext7.com/tools/openmm
AMBER (Assisted Model Building with Energy Refinement) — suite of molecular dynamics simulation programs for biomolecular systems. Provides force fields (ff14SB, ff19SB, GAFF2), system preparation (tl
1 shared topic • 3 shared operations
Deep learning system for protein structure prediction from amino acid sequence with atomic accuracy — revolutionized structural biology.
1 shared topic • 2 shared operations
Boltz-1 — open-source deep learning model for predicting biomolecular 3D structures and interactions, approaching AlphaFold3-level accuracy. Supports protein, DNA, RNA, and small-molecule ligand struc
1 shared topic • 2 shared operations
Ensembl Database — EMBL-EBI's comprehensive genome annotation database covering 300+ species with gene models, variants, regulatory features, and comparative genomics. Query via REST API at rest.ensem
1 shared topic • 2 shared operations
Direct REST API access to UniProt (250M+ protein sequences, 570K+ reviewed Swiss-Prot entries). Protein search, FASTA/JSON retrieval, ID mapping across 200+ databases, batch retrieval, streaming, fiel
1 shared topic • 2 shared operations