RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

Abstract

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with >40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic.

PDBcle – An online tool for extracting chain structure and sequence of macromolecule and small molecule structure from the Protein Data Bank

“…Separate PDB files are generated for DNA molecule by combining the atom records of two chains in pair or group according to the molecule type. The molecules in the PDB repository are categorized as a polypeptide, polydeoxyribonucleotide, cyclic-pseudo-peptide, polysaccharide, polydeoxyribonucleotide/ polyribonucleotide hybrid, polyribonucleotide, and small molecules (2)(3)(4) . The PDB cle tool splits the chains in the molecule under three major categories, (1) macromolecule, (2) macromolecule and small molecule complex, and (3) small molecule (Table 2 ).…”

“…Moreover, the wwPDB has stopped modifying or extending the data dictionary of the PDB file format. The PDBx/mmCIF file format is considered as standard PDB archive format and PDBML/XML file format for programming purposes (1)(2)(3) . PDB cle tool was designed to generate a 3D template structure (biomolecule chains) in PDB file format and retrieve compounds in SDF file format from PDB sever through parsing the PDBML/XML file.…”

Computational evaluation of interactions between olfactory receptor OR2W1 and its ligands

“…The amino acid sequence for OR2W1 (UniProt: Q9Y3N9) was obtained from UniProt Knowl-edgeBase (https://www.uniprot.org/) [7]. To pick out the amino acid sequences of 7TMRs with a higher BLAST score (Bits) than 45 or a lower E-value than 1e-07 [8,9], we analyzed the amino acid sequence of OR2W1 against the locally-built BLAST database of 7TMR amino acid sequences registered in the RCSB Protein Data Bank (PDB) [10,11]. Based on their similarity results for OR2W1, four PDB entries of three 7TMRs were selected as the experimental templates for the homology modeling of OR2W1: human serotonin receptor (HTR2A), bovine rhodopsin (Rho), and two turkey β1-adrenoceptor (ADRB1) PDB models.…”

Deep Learning in Virtual Screening: Recent Applications and Developments

“…Furthermore, a considerable amount of structural data has also been published over the last decades. The freely available Protein Data Bank (PDB) [ 38 , 39 ] logged 14,047 new entries in 2020. In March 2021, the total number of available entries has surpassed 175,000 [ 40 ] and will most probably keep increasing.…”