Publications by authors named "Benjamin M Webb"

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IHMValidation: Assessment of Integrative Structure Models Deposited to the Protein Data Bank.
Arthur O Zalevsky, Brinda Vallat, Benjamin M Webb, Hongsuda Tangmunarunkit, Monica R Sekharan

J Mol Biol· December 2025

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RCSB Protein Data Bank: Delivering integrative structures alongside experimental structures and computed structure models.
Brinda Vallat, Yana Rose, Dennis W Piehl, Jose M Duarte, Sebastian Bittrich, Benjamin M Webb

Nucleic Acids Res· November 2025

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PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures.
Brinda Vallat, Benjamin M Webb, Arthur Zalevsky, Hongsuda Tangmunarunkit, Monica R Sekharan

J Mol Biol· August 2025

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Recognizing amino acid sidechains in a medium-resolution cryo-electron density map.
Dibyendu Mondal, Vipul Kumar, Tadej Satler, Rakesh Ramachandran, Daniel Saltzberg, Benjamin M Webb

Protein Sci· August 2025

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Recognizing amino acid sidechains in a medium resolution cryo-electron density map.
Dibyendu Mondal, Vipul Kumar, Tadej Satler, Rakesh Ramachandran, Daniel Saltzberg, Benjamin M Webb

bioRxiv· May 2025

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Tutorial on integrative spatiotemporal modeling by integrative modeling platform.
Andrew P Latham, Miha Rožič, Benjamin M Webb, Andrej Sali

Protein Sci· April 2025

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tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling.
Thomas-Otavio Peulen, Katherina Hemmen, Annemarie Greife, Benjamin M Webb, Suren Felekyan

Bioinformatics· February 2025

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Making fluorescence-based integrative structures and associated kinetic information accessible.
Christian A Hanke, John D Westbrook, Benjamin M Webb, Thomas-O Peulen, Catherine L Lawson

Nat Methods· November 2024

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IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods.
Brinda Vallat, Benjamin M Webb, John D Westbrook, Thomas D Goddard, Christian A Hanke

J Mol Biol· September 2024

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ModelCIF: An Extension of PDBx/mmCIF Data Representation for Computed Structure Models.
Brinda Vallat, Gerardo Tauriello, Stefan Bienert, Juergen Haas, Benjamin M Webb

J Mol Biol· July 2023

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ModBase, a database of annotated comparative protein structure models and associated resources.
Ursula Pieper, Benjamin M Webb, Guang Qiang Dong, Dina Schneidman-Duhovny, Hao Fan

Nucleic Acids Res· January 2014

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Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images.
Javier Velázquez-Muriel, Keren Lasker, Daniel Russel, Jeremy Phillips, Benjamin M Webb

Proc Natl Acad Sci U S A· November 2012

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SALIGN: a web server for alignment of multiple protein sequences and structures.
Hannes Braberg, Benjamin M Webb, Elina Tjioe, Ursula Pieper, Andrej Sali

Bioinformatics· August 2012

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Macromolecular assembly structures by comparative modeling and electron microscopy.
Keren Lasker, Javier A Velázquez-Muriel, Benjamin M Webb, Zheng Yang, Thomas E Ferrin

Methods Mol Biol· May 2012

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ModBase, a database of annotated comparative protein structure models, and associated resources.
Ursula Pieper, Benjamin M Webb, David T Barkan, Dina Schneidman-Duhovny, Avner Schlessinger

Nucleic Acids Res· January 2011

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Molecular docking screens using comparative models of proteins.
Hao Fan, John J Irwin, Benjamin M Webb, Gerhard Klebe, Brian K Shoichet

J Chem Inf Model· November 2009

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Alignment of multiple protein structures based on sequence and structure features.
M S Madhusudhan, Benjamin M Webb, Marc A Marti-Renom, Narayanan Eswar, Andrej Sali

Protein Eng Des Sel· September 2009

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