Protein Data Bank - an overview | ScienceDirect Topics
The Protein Data Bank (PDB) is an open-access database that saves and distributes (3D) biomolecular structure information to assist in the exploration and design of therapeutic and diagnostic equipment.
RCSB Protein Data Bank: Architectural Advances Towards Integrated ...
May 28, 2021 · These ETL operations include updates to reference sequence database correspondences plus reference database correspondences for small molecules in PDB chemical …
Databases of ligand-binding pockets and protein-ligand interactions
Dec 1, 2024 · Het-PDB Navi [107] is a database of small molecule interactions present in the PDB. In addition to providing information on ligands and interacting residues for each included PDB structure, …
RCSB Protein Data Bank: Efficient Searching and ... - ScienceDirect
Jul 15, 2023 · The Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank (PDB) RCSB.org research-focused web portal 1, 2, 3 provides open access to a rigorously validated, …
OPRLM: A Web Tool and a Database for Positioning and Simulations of ...
Aug 1, 2025 · For all selected hetero chains from RCSB PDB or OPRLM entries, the server systematically retrieves associated SDF files from the RCSB PDB database for each ligand and …
AlphaFold Protein Structure Database and 3D-Beacons: New Data and ...
Aug 1, 2025 · The AlphaFold Protein Database Updates Structural similarity analysis with Foldseek The AlphaFold Protein Structure Database provides an unprecedented breadth of structure data, …
PSAC-PDB: Analysis and classification of protein structures
May 1, 2023 · This paper presents a novel framework, called PSAC-PDB, for analyzing and classifying protein structures from the Protein Data Bank (PDB). PSAC-PDB first finds, analyze and identifies …
PDID: Database of Experimental and Putative Drug Targets in Human ...
The template proteins come from a database of templates, typically defined as a set of nonredundant high-quality structures of drug-protein complexes curated from the PDB database; e FindSite also …
Alpha&ESMhFolds: A Web Server for Comparing AlphaFold2 and …
Sep 1, 2024 · Abstract We develop a novel database Alpha&ESMhFolds which allows the direct comparison of AlphaFold2 and ESMFold predicted models for 42,942 proteins of the Reference …
RNA3DB: A structurally-dissimilar dataset split for training and ...
Sep 1, 2024 · RNA3DB is a dataset based on all PDB RNA 3D structures developed for addressing the aforementioned concerns, especially those regarding generalization, particularly for training and …