Results for “pdb”
6 skills
k-dense-ai biopython
Manipulate biological sequences, parse FASTA/GenBank/PDB files, access NCBI databases, run BLAST searches, and perform phylogenetics using the Biopython library.
30.2k · bundle
lucaspmarie-a11y biopython
Provides reference documentation and code patterns for Biopython, covering sequence handling, alignments, NCBI database access, BLAST, protein structures, phylogenetics, and other bioinformatics tasks.
5
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k-dense-ai diffdock
Predict 3D binding poses of small molecule ligands to protein targets using diffusion-based molecular docking, supporting single complexes, batch processing, and virtual screening.
30.2k · bundle
tradermonty stockbee-episodic-pivot-analyzer
Analyzes Stockbee-style Day 1 Episodic Pivot candidates by scoring catalyst quality alongside price/volume confirmation, gap/range expansion, volume shock, neglect/revaluation context, liquidity, and risk to the EP-day low.
2.3k · bundle
alterlab-ieu alterlab-pubmed
Provide direct REST API access to PubMed via the NCBI E-utilities API, supporting advanced Boolean/MeSH queries, batch processing, and citation management. Use when searching biomedical literature by MeSH terms, retrieving abstracts or PMIDs in bulk, or scripting custom PubMed queries over raw HTTP/REST — for Python workflows prefer biopython (Bio.Entrez) instead, use this for direct REST work or custom API implementations. Part of the AlterLab Academic Skills suite.
60 · bundle
k-dense-ai molecular-dynamics
Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces).
30.2k · bundle