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Brinda K. Vallat · SciRah

Researcher profile · Semantic Scholar

Brinda K. Vallat

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Brinda K. Vallat — researcher profile on SciRah

h-index: 20
Works: 55
Citations: 2,377

Most-cited papers

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
S. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich +37 more
2022Nucleic Acids Res.776 citations Open access
Semantic Scholar
Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank
Stephen K. Burley, Rusham Bhatt, Charmi Bhikadiya, Chunxiao Bi +47 more
2024Nucleic Acids Research353 citations Open access
Semantic Scholar
RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D
S. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich +31 more
2021Protein Science189 citations Open access
Semantic Scholar
RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D
S. Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich +37 more
2022Protein Science113 citations Open access
Semantic Scholar
Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students
S. Burley, H. Berman, Jose M. Duarte, Zu-Kang Feng +14 more
2022Biomolecules112 citations Open access
Semantic Scholar
SOD1 Phosphorylation by mTORC1 Couples Nutrient Sensing and Redox Regulation
Chi-Kwan Tsang, Miao Chen, Xin Cheng, Yan-Mei Qi +10 more
2018Molecules and Cells111 citations Open access
Semantic Scholar
Development of a prototype system for archiving integrative/hybrid structure models of biological macromolecules
Brinda K. Vallat, Ben M. Webb, J. Westbrook, A. Sali +1 more
2018Structure90 citations Open access
Semantic Scholar
RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Models Alongside the PDB Structures Enabled by Architectural Advances
Sebastian Bittrich, Charmi Bhikadiya, Chunxiao Bi, Henry Chao +13 more
2023Journal of Molecular Biology73 citations Open access
Semantic Scholar
PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology
J. Westbrook, Jasmine Y. Young, C. Shao, Zu-Kang Feng +18 more
2022Journal of Molecular Biology71 citations Open access
Semantic Scholar
The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids
Catherine L. Lawson, H. Berman, Li Chen, Brinda K. Vallat +1 more
2023Nucleic Acids Research69 citations Open access
Semantic Scholar
RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures
Stephen K. Burley, Dennis W. Piehl, Brinda K. Vallat, C. Zardecki
2024IUCrJ48 citations Open access
Semantic Scholar
FEDERATING STRUCTURAL MODELS AND DATA: OUTCOMES FROM A WORKSHOP ON ARCHIVING INTEGRATIVE STRUCTURES
H. Berman, P. Adams, Alexandre Bonvin, S. Burley +34 more
2019Structure43 citations Open access
Semantic Scholar
RCSB Protein Data Bank: Delivering integrative structures alongside experimental structures and computed structure models
Brinda K. Vallat, Yana Rose, Dennis W. Piehl, Jose M. Duarte +22 more
2025Nucleic Acids Research39 citations Open access
Semantic Scholar
A Novel Acquired Exon 20 EGFR M766Q Mutation in Lung Adenocarcinoma Mediates Osimertinib Resistance but is Sensitive to Neratinib and Poziotinib: a Brief Report
G. Castellano, J. Aisner, S. Burley, Brinda K. Vallat +3 more
2019Journal of Thoracic Oncology32 citations Open access
Semantic Scholar
Building and assessing atomic models of proteins from structural templates: Learning and benchmarks
Brinda K. Vallat, J. Pillardy, P. Májek, J. Meller +3 more
2009Proteins: Structure, Function, and Bioinformatics28 citations Open access
Semantic Scholar
Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution, new validation tools, and implications for the future
S. Burley, H. Berman, Wah Chiu, W. Dai +12 more
2022Biophysical Reviews27 citations Open access
Semantic Scholar
Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures
Brinda K. Vallat, Carlos J. Madrid-Aliste, A. Fiser
2015PLoS Comput. Biol.25 citations Open access
Semantic Scholar
New system for archiving integrative structures
Brinda K. Vallat, Ben M. Webb, M. Fayazi, Serban Voinea +7 more
2021Acta Crystallographica Section D: Structural Biology24 citations Open access
Semantic Scholar
A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins
Brinda K. Vallat, J. Pillardy, R. Elber
2008Proteins: Structure, Function, and Bioinformatics22 citations Open access
Semantic Scholar
Archiving and disseminating integrative structure models
Brinda K. Vallat, Ben M. Webb, J. Westbrook, A. Sali +1 more
2019Journal of Biomolecular NMR20 citations Open access
Semantic Scholar
ModelCIF: An extension of PDBx/mmCIF data representation for computed structure models
Brinda K. Vallat, G. Tauriello, S. Bienert, J. Haas +21 more
2022bioRxiv19 citations Open access
Semantic Scholar
Modeling proteins using a super-secondary structure library and NMR chemical shift information
V. Menon, Brinda K. Vallat, Joseph M. Dybas, A. Fiser
2013Structure15 citations Open access
Semantic Scholar
The data universe of structural biology
H. Berman, Brinda K. Vallat, C. Lawson
2020IUCrJ14 citations Open access
Semantic Scholar
PDB-IHM: A system for deposition, curation, validation, and dissemination of integrative structures
Brinda K. Vallat, Benjamin M. Webb, Arthur O. Zalevsky, H. Tangmunarunkit +12 more
2025Journal of Molecular Biology12 citations Open access
Semantic Scholar
IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods
Brinda K. Vallat, Ben M. Webb, J. Westbrook, T. Goddard +31 more
2024Journal of Molecular Biology11 citations Open access
Semantic Scholar
Fast Geometric Consensus Approach for Protein Model Quality Assessment
R. Adamczak, J. Pillardy, Brinda K. Vallat, J. Meller
2011J. Comput. Biol.7 citations Open access
Semantic Scholar
rcsb-api: Python Toolkit for Streamlining Access to RCSB Protein Data Bank APIs
Dennis W. Piehl, Brinda K. Vallat, Ivana Truong, Habiba Morsy +12 more
2025Journal of Molecular Biology6 citations Open access
Semantic Scholar
Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit
Sebastian Bittrich, Adam Midlik, M. Váradi, S. Velankar +4 more
2024Current Protocols6 citations Open access
Semantic Scholar
Making fluorescence-based integrative structures and associated kinetic information accessible
Christian A. Hanke, J. Westbrook, Ben M. Webb, Thomas O. Peulen +5 more
2024Nature Methods6 citations
Semantic Scholar
MolViewSpec: a Mol* extension for describing and sharing molecular visualizations
Adam Midlik, Sebastian Bittrich, Jennifer R. Fleming, S. Nair +5 more
2025Nucleic Acids Research5 citations Open access
Semantic Scholar
Archiving of Integrative Structural Models.
H. Berman, J. Trewhella, Brinda K. Vallat, J. Westbrook
2018Advances in Experimental Medicine and Biology5 citations
Semantic Scholar
ANTICIPATING INNOVATIONS IN STRUCTURAL BIOLOGY
H. Berman, C. Lawson, Brinda K. Vallat, M. Gabanyi
2018Quarterly Reviews of Biophysics (print)5 citations Open access
Semantic Scholar
Structural highlights of macromolecular complexes and assemblies.
Brinda K. Vallat, Helen M. Berman
2024Current Opinion in Structural Biology3 citations Open access
Semantic Scholar
Database Evolution, by Scientists, for Scientists: A Case Study
R. Schuler, Jitin Singla, Brinda K. Vallat, Kate L. White +2 more
2023IEEE International Conference on e-Science3 citations
Semantic Scholar
Protein Data Bank (PDB) Archive: a new architecture (beta) for scalable, PDBx/mmCIF-based data distribution
Zu-Kang Feng, Balakumaran Balasubramaniyan, G. Bekker, Jose M. Duarte +16 more
2026Acta Crystallographica Section D: Structural Biology2 citations Open access
Semantic Scholar
IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank
Arthur O. Zalevsky, Brinda K. Vallat, Benjamin M. Webb, H. Tangmunarunkit +23 more
2025Journal of Molecular Biology2 citations Open access
Semantic Scholar
Visualizing and analyzing 3D biomolecular structures using Mol* at RCSB.org: Influenza A H5N1 virus proteome case study
Sebastian Bittrich, Alexander S Rose, David Sehnal, Jose M. Duarte +11 more
2025Protein Science2 citations Open access
Semantic Scholar
A data dictionary for archiving integrative/hybrid models
Brinda K. Vallat, Ben M. Webb, J. Westbrook, A. Sali +1 more
20172 citations Open access
Semantic Scholar
ModelCIF Update: Supporting Emerging Classes of Computational Macromolecular Models
G. Tauriello, Y. Lill, Jacopo Sgrignani, Vincent Zoete +13 more
2026Journal of Molecular Biology1 citations Open access
Semantic Scholar
PDBx/mmCIF Ecosystem: Foundation for FAIR Access to Macromolecular Structure Data
Brinda K. Vallat
2025Structural Dynamics1 citations Open access
Semantic Scholar
PDB-IHM: A System for Archiving and Dissemination of integrative structures
Brinda K. Vallat
2025Structural Dynamics1 citations Open access
Semantic Scholar
Abstract 617: OSTM1 is a ubiquitin E3 ligase that suppresses B-cell malignancy by activating the cAMP/PKA pathway.
Muhammad Usama Tariq, Namratha Sheshadri, Julia Shen, Jaeyong Jung +18 more
2026Cancer Research0 citations
Semantic Scholar
Abstract A035: ER-associated retrotranslocation generates a cytosolic OSTM1 E3 ubiquitin ligase that targets PDE3B for degradation
Hassan Sajjad, Muhammad Usama Tariq, Jianliang Shen, Rongrong Li +9 more
2026Blood Cancer Discovery0 citations
Semantic Scholar
BPS2026 – RCSB protein data bank: Delivering integrative structures alongside experimental structures and computed structure models
Brinda K. Vallat
2026Biophysical Journal0 citations
Semantic Scholar
MolViewStories: Interactive molecular storytelling
Terézia Slanináková, Z. Charlop-Powers, Viktoriia Doshchenko, Alexander S Rose +10 more
2026Protein Science0 citations Open access
Semantic Scholar
OSTM1 is a ubiquitin E3 ligase that suppresses B-cell malignancy by activating the cAMP/PKA/CREB pathway
Muhammad Usama Tariq, Namratha Sheshadri, Jianliang Shen, Jaeyong Jung +19 more
2026bioRxiv0 citations
Semantic Scholar
PDB-Dev: a prototype system for archiving integrative structures
Brinda K. Vallat, Ben M. Webb, Arthur O. Zalevsky, Serban Voinea +7 more
2023Acta Crystallographica Section A: Foundations and Advances0 citations Open access
Semantic Scholar
Exploring experimental structures and computed structure models from artificial intelligence/machine learning at RCSB Protein Data Bank (RCSB PDB, RCSB.org).
J. Segura, Jose M. Duarte, Sebastian Bittrich, Chunxiao Bi +11 more
2023Biophysical Journal0 citations Open access
Semantic Scholar
Archiving Integrative Structural Models
Brinda K. Vallat, Ben M. Webb, J. Westbrook, H. Tangmunarunkit +4 more
20210 citations Open access
Semantic Scholar
BioExcel Webinar #45 - PDB-Dev: A prototype system for archiving integrative structures
Brinda K. Vallat, Ben M. Webb
20200 citations
Semantic Scholar

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