A5061045572- Enzyme Structure and Function
- Protein Structure and Dynamics
- Genetics, Bioinformatics, and Biomedical Research
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- Scientific Computing and Data Management
- Machine Learning in Bioinformatics
- Advanced Proteomics Techniques and Applications
- Computational Drug Discovery Methods
- Microtubule and mitosis dynamics
- RNA and protein synthesis mechanisms
- Microbial Metabolic Engineering and Bioproduction
- Statistical Methods in Clinical Trials
- Protein Tyrosine Phosphatases
- Glycosylation and Glycoproteins Research
- Distributed and Parallel Computing Systems
- Gene expression and cancer classification
- RFID technology advancements
- Algorithms and Data Compression
- QR Code Applications and Technologies
San Diego Supercomputer Center
2017-2025
University of California, San Diego
2017-2025
University of San Diego
2023
Rutgers Sexual and Reproductive Health and Rights
2021
TD Bank
2021
Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center global PDB archive and a founding member of Worldwide partnership, serves tens thousands depositors in Americas Oceania makes 3D macromolecular structure available at no charge without restrictions to millions RCSB.org users around world, including >660 000 educators, students members curious public using PDB101.RCSB.org. include structural biologists crystallography,...
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), founding member of the Worldwide (wwPDB), is US data center open-access PDB archive. As wwPDB-designated Archive Keeper, RCSB also responsible security. Annually, serves >10 000 depositors three-dimensional (3D) biostructures working on all permanently inhabited continents. delivers from its research-focused RCSB.org web portal to many millions consumers based in virtually every United Nations-recognized...
The US Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves many millions of unique users worldwide by delivering experimentally-determined 3D structures biomolecules integrated with >40 external data resources via RCSB.org, application programming interfaces (APIs), and FTP downloads. Herein, we present the architectural redesign RCSB PDB delivery services that build on existing PDBx/mmCIF schemas. New access APIs (data.rcsb.org) enable efficient all...
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, Institutes of Health, and Department Energy, has served structural biologists (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member Worldwide (wwPDB) partnership, is center global PDB archive housing biomolecular structure data. also responsible security data, as wwPDB-designated Archive Keeper. Annually, serves tens thousands three-dimensional...
Abstract Motivation Tools for pairwise alignments between 3D structures of proteins are fundamental importance structural biology and bioinformatics, enabling visual exploration evolutionary functional relationships. However, the absence a user-friendly, browser-based tool creating visualizing them at both 1D sequence levels makes this process unnecessarily cumbersome. Results We introduce novel structure alignment (rcsb.org/alignment) that seamlessly integrates into RCSB Protein Data Bank...
Abstract Motivation Membrane proteins are encoded by approximately one fifth of human genes but account for more than half all US FDA approved drug targets. Thanks to new technological advances, the number membrane archived in PDB is growing rapidly. However, automatic identification or inference location not a trivial task. Results We present recent improvements RCSB Protein Data Bank web portal (RCSB PDB, rcsb.org) that provide wealth protein annotations integrated from four external...
Abstract Now in its 52nd year of continuous operations, the Protein Data Bank (PDB) is premiere open‐access global archive housing three‐dimensional (3D) biomolecular structure data. It jointly managed by Worldwide (wwPDB) partnership. The Research Collaboratory for Structural Bioinformatics (RCSB PDB) funded National Science Foundation, Institutes Health, and US Department Energy serves as data center wwPDB. RCSB PDB also responsible security role wwPDB‐designated Archive Keeper. Every...
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) provides open access to experimentally-determined three-dimensional (3D) structures of biomolecules. RCSB PDB RCSB.org research-focused web portal is used annually by many millions users around the world. They biostructure information, run complex queries utilizing various search services (e.g., full-text, structural and chemical attribute, chemical, sequence, structure similarity searches), visualize...
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide (wwPDB, wwPDB.org) data center global PDB archive, provides access to via its RCSB.org research-focused web portal. We report substantial additions tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in archive alongside 1 million Computed Structure Models...
Abstract The rapid expansion of three-dimensional (3D) biomolecular structure information, driven by breakthroughs in artificial intelligence/deep learning (AI/DL)-based predictions, has created an urgent need for scalable and efficient similarity search methods. Traditional alignment-based approaches, such as structural superposition tools, are computationally expensive challenging to scale with the vast number available macromolecular structures. Herein, we present a strategy designed...
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 RCSB Protein Data Bank (RCSB PDB, RCSB.org ) in Europe (PDBe, PDBe.org as an open‐source, web‐based, 3D software suite for examination analyses biostructures. It capable displaying atomic coordinates related experimental data...
Interoperability between polymer sequences and structural data is essential for providing a complete picture of protein gene features helping to understand biomolecular function.Herein, we present two resources designed improve interoperability the RCSB Protein Data Bank, NCBI UniProtKB visualize integrated therefrom. The underlying tools provide flexible means mapping different coordinate spaces an interactive tool allows convenient visualization 1-dimensional over...
Recent advances in Artificial Intelligence and Machine Learning (
Abstract Motivation Mapping positional features from one-dimensional (1D) sequences onto three-dimensional (3D) structures of biological macromolecules is a powerful tool to show geometric patterns biochemical annotations and provide better understanding the mechanisms underpinning protein nucleic acid function at atomic level. Results We present new library designed display fully customizable interactive views between 1D and/or their 3D as isolated chains or components macromolecular...
Abstract Recent advances in experimental techniques have led to a rapid growth complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates challenge for visualization analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow transfer, parse, hard incorporate into third-party software tools. Here, we present new binary compressed data representation, MacroMolecular Transmission Format, MMTF, well...