Results for “pdb”

Primary Python toolkit for molecular biology. Preferred for Python-based PubMed/NCBI queries (Bio.Entrez), sequence manipulation, file parsing (FASTA, GenBank, FASTQ, PDB), advanced BLAST workflows, structures, phylogenetics. For quick BLAST, use gget. For direct REST API, use pubmed-database.

PDN DC voltage/current analysis, IR drop, design rule checking, and multi-net batch analysis on imported PCB layouts. TRIGGER: user asks about power integrity, PDN analysis, IR drop, voltage distribution, current density, power nets, or design rule checking on a PCB. Invoke BEFORE writing code — the PDN API chain is specialized and non-obvious. SKIP: importing a PCB file (use matlab-read-pcb-layout), EM field/S-parameter extraction (use matlab-analyze-em), material/stackup setup only (use matlab-manage-pcb-material), transmission line design (use matlab-design-pcb-transmission-line).

Query BindingDB for measured protein-ligand binding affinities (Ki, Kd, IC50, EC50) via its keyless REST API or the full TSV download, searching by target (UniProt ID), compound (SMILES), or pathogen. Use when looking up experimental binding constants, profiling inhibitors of a protein target, doing lead optimization, polypharmacology analysis, or structure-activity relationship (SAR) studies; for curated bioactivity mining or drug-like compound library screening at scale prefer alterlab-chembl instead. Part of the AlterLab Academic Skills suite.

MongoDB - NoSQL document database with flexible schema design, aggregation pipelines, indexing strategies, and Spring Data integration

Provide direct REST API access to UniProt (Swiss-Prot/TrEMBL) for protein sequence searches, FASTA retrieval, functional annotations (GO terms, domains), and cross-database ID mapping. Use when looking up a protein entry, fetching a protein FASTA sequence, or mapping accessions between databases over raw HTTP/REST; for EXPERIMENTAL 3D structures prefer alterlab-pdb, for AI-PREDICTED 3D structures prefer alterlab-alphafold-db, for protein-protein interaction networks prefer alterlab-string-db, and for Python workflows spanning many databases prefer bioservices instead. Part of the AlterLab Academic Skills suite.