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1. RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments

   https://doi.org/10.1093/bioinformatics/btae370  

   Bittrich, Sebastian ; Segura, Joan ; Duarte, Jose_M ; Burley, Stephen_K ; Rose, Yana ; Elofsson, ed., Arne ( June 2024 , Bioinformatics)

   Tools for pairwise alignments between 3D structures of proteins are of fundamental importance for structural biology and bioinformatics, enabling visual exploration of evolutionary and functional relationships. However, the absence of a user-friendly, browser-based tool for creating alignments and visualizing them at both 1D sequence and 3D structural levels makes this process unnecessarily cumbersome.

   We introduce a novel pairwise structure alignment tool (rcsb.org/alignment) that seamlessly integrates into the RCSB Protein Data Bank (RCSB PDB) research-focused RCSB.org web portal. Our tool and its underlying application programming interface (alignment.rcsb.org) empowers users to align several protein chains with a reference structure by providing access to established alignment algorithms (FATCAT, CE, TM-align, or Smith–Waterman 3D). The user-friendly interface simplifies parameter setup and input selection. Within seconds, our tool enables visualization of results in both sequence (1D) and structural (3D) perspectives through the RCSB PDB RCSB.org Sequence Annotations viewer and Mol* 3D viewer, respectively. Users can effortlessly compare structures deposited in the PDB archive alongside more than a million incorporated Computed Structure Models coming from the ModelArchive and AlphaFold DB. Moreover, this tool can be used to align custom structure data by providing a link/URL or uploading atomic coordinate files directly. Importantly, alignment results can be bookmarked and shared with collaborators. By bridging the gap between 1D sequence and 3D structures of proteins, our tool facilitates deeper understanding of complex evolutionary relationships among proteins through comprehensive sequence and structural analyses.

   The alignment tool is part of the RCSB PDB research-focused RCSB.org web portal and available at rcsb.org/alignment. Programmatic access is available via alignment.rcsb.org. Frontend code has been published at github.com/rcsb/rcsb-pecos-app. Visualization is powered by the open-source Mol* viewer (github.com/molstar/molstar and github.com/molstar/rcsb-molstar) plus the Sequence Annotations in 3D Viewer (github.com/rcsb/rcsb-saguaro-3d).

    

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2. 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)

   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.

    

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3. RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D

   https://doi.org/10.1002/pro.4213  

   Burley, Stephen K. ; Bhikadiya, Charmi ; Bi, Chunxiao ; Bittrich, Sebastian ; Chen, Li ; Crichlow, Gregg V. ; Duarte, Jose M. ; Dutta, Shuchismita ; Fayazi, Maryam ; Feng, Zukang ; et al ( November 2021 , Protein Science)

   The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB‐designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three‐dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro‐electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research‐focusedRCSB.orgweb portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and educationPDB101.RCSB.orgweb portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past yearviatheRCSB.orgweb portal.

    

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4. 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 ( November 2024 , Nucleic Acids Research)

   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.

    

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5. BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank

   https://doi.org/10.1093/bioinformatics/btx101  

   Gao, Jianjiong ; Prlić, Andreas ; Bi, Chunxiao ; Bluhm, Wolfgang F. ; Dimitropoulos, Dimitris ; Xu, Dong ; Bourne, Philip E. ; Rose, Peter W. ; Valencia, ed., Alfonso ( February 2017 , Bioinformatics)

   We developed a new software tool, BioJava-ModFinder, for identifying protein modifications observed in 3D structures archived in the Protein Data Bank (PDB). Information on more than 400 types of protein modifications were collected and curated from annotations in PDB, RESID, and PSI-MOD. We divided these modifications into three categories: modified residues, attachment modifications, and cross-links. We have developed a systematic method to identify these modifications in 3D protein structures. We have integrated this package with the RCSB PDB web application and added protein modification annotations to the sequence diagram and structure display. By scanning all 3D structures in the PDB using BioJava-ModFinder, we identified more than 30 000 structures with protein modifications, which can be searched, browsed, and visualized on the RCSB PDB website.

   BioJava-ModFinder is available as open source (LGPL license) at (https://github.com/biojava/biojava/tree/master/biojava-modfinder). The RCSB PDB can be accessed at http://www.rcsb.org.

    

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