More Like this

1. RCSB Protein Data Bank: improved annotation, search and visualization of membrane protein structures archived in the PDB

   https://doi.org/10.1093/bioinformatics/btab813  

   Bittrich, Sebastian; Rose, Yana; Segura, Joan; Lowe, Robert; Westbrook, John D; Duarte, Jose M; Burley, Stephen K (December 2021, Bioinformatics)

   Valencia, Alfonso (Ed.)

   Abstract Motivation Membrane proteins are encoded by approximately one fifth of human genes but account for more than half of all US FDA approved drug targets. Thanks to new technological advances, the number of membrane proteins archived in the PDB is growing rapidly. However, automatic identification of membrane proteins or inference of membrane location is not a trivial task. Results We present recent improvements to the RCSB Protein Data Bank web portal (RCSB PDB, rcsb.org) that provide a wealth of new membrane protein annotations integrated from four external resources: OPM, PDBTM, MemProtMD and mpstruc. We have substantially enhanced the presentation of data on membrane proteins. The number of membrane proteins with annotations available on rcsb.org was increased by ∼80%. Users can search for these annotations, explore corresponding tree hierarchies, display membrane segments at the 1D amino acid sequence level, and visualize the predicted location of the membrane layer in 3D. Availability and implementation Annotations, search, tree data and visualization are available at our rcsb.org web portal. Membrane visualization is supported by the open-source Mol* viewer (molstar.org and github.com/molstar/molstar). Supplementary information Supplementary data are available at Bioinformatics online. 

   more » « less
2. Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study

   https://doi.org/10.1002/pro.70093  

   Bittrich, Sebastian; Rose, Alexander S; Sehnal, David; Duarte, Jose M; Rose, Yana; Segura, Joan; Piehl, Dennis W; Vallat, Brinda; Shao, Chenghua; Bhikadiya, Charmi; et al (April 2025, Protein Science)

   Abstract The easiest and often most useful way to work with experimentally determined or computationally predicted structures of biomolecules is by viewing their three‐dimensional (3D) shapes using a molecular visualization tool. Mol* was collaboratively developed by RCSB Protein Data Bank (RCSB PDB,RCSB.org) and Protein Data Bank in Europe (PDBe,PDBe.org) as an open‐source, web‐based, 3D visualization software suite for examination and analyses of biostructures. It is capable of displaying atomic coordinates and related experimental data of biomolecular structures together with a variety of annotations, facilitating basic and applied research, training, education, and information dissemination. AcrossRCSB.org, the RCSB PDB research‐focused web portal, Mol* has been implemented to support single‐mouse‐click atomic‐level visualization of biomolecules (e.g., proteins, nucleic acids, carbohydrates) with bound cofactors, small‐molecule ligands, ions, water molecules, or other macromolecules.RCSB.orgMol* can seamlessly display 3D structures from various sources, allowing structure interrogation, superimposition, and comparison. Using influenza A H5N1 virus as a topical case study of an important pathogen, we exemplify how Mol* has been embedded within variousRCSB.orgtools—allowing users to view polymer sequence and structure‐based annotations integrated from trusted bioinformatics data resources, assess patterns and trends in groups of structures, and view structures of any size and compositional complexity. In addition to being linked to every experimentally determined biostructure and Computed Structure Model made available atRCSB.org, Standalone Mol* is freely available for visualizing any atomic‐level or multi‐scale biostructure atrcsb.org/3d-view. 

   more » « less
3. RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning

   https://doi.org/10.1093/nar/gkac1077  

   Burley, Stephen K; Bhikadiya, Charmi; Bi, Chunxiao; Bittrich, Sebastian; Chao, Henry; Chen, Li; Craig, Paul A; Crichlow, Gregg V; Dalenberg, Kenneth; Duarte, Jose M; et al (November 2022, Nucleic Acids Research)

   Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide Protein Data Bank (wwPDB), is the US data center for the open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB PDB is also responsible for PDB data security. Annually, RCSB PDB serves >10 000 depositors of three-dimensional (3D) biostructures working on all permanently inhabited continents. RCSB PDB delivers data from its research-focused RCSB.org web portal to many millions of PDB data consumers based in virtually every United Nations-recognized country, territory, etc. This Database Issue contribution describes upgrades to the research-focused RCSB.org web portal that created a one-stop-shop for open access to ∼200 000 experimentally-determined PDB structures of biological macromolecules alongside >1 000 000 incorporated Computed Structure Models (CSMs) predicted using artificial intelligence/machine learning methods. RCSB.org is a ‘living data resource.’ Every PDB structure and CSM is integrated weekly with related functional annotations from external biodata resources, providing up-to-date information for the entire corpus of 3D biostructure data freely available from RCSB.org with no usage limitations. Within RCSB.org, PDB structures and the CSMs are clearly identified as to their provenance and reliability. Both are fully searchable, and can be analyzed and visualized using the full complement of RCSB.org web portal capabilities. 

   more » « less
4. RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins

   https://doi.org/10.3389/fbinf.2023.1311287  

   Segura, Joan; Rose, Yana; Bi, Chunxiao; Duarte, Jose; Burley, Stephen K.; Bittrich, Sebastian (December 2023, Frontiers in Bioinformatics)

   Recent advances in Artificial Intelligence and Machine Learning (e.g., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information. Given the enormous volume of this newly computed biostructure data, there is an urgent need for robust tools to manage, search, cluster, and visualize large collections of structures. Equally important is the capability to efficiently summarize and visualize metadata, biological/biochemical annotations, and structural features, particularly when working with vast numbers of protein structures of both experimental origin from the Protein Data Bank (PDB) and computationally-predicted models. Moreover, researchers require advanced visualization techniques that support interactive exploration of multiple sequences and structural alignments. This paper introduces a suite of tools provided on the RCSB PDB research-focused web portal RCSB. org, tailor-made for efficient management, search, organization, and visualization of this burgeoning corpus of 3D macromolecular structure data. 

   more » « less
5. Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

   https://doi.org/10.1093/nar/gkae1091  

   Burley, Stephen K; Bhatt, Rusham; Bhikadiya, Charmi; Bi, Chunxiao; Biester, Alison; Biswas, Pratyoy; Bittrich, Sebastian; Blaumann, Santiago; Brown, Ronald; Chao, Henry; et al (January 2025, Nucleic Acids Research)

   Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities. 

   more » « less