Jose M. Duarte

发表

RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy

David S. Goodsell, Zukang Feng, John D. Westbrook, 2018, Nucleic Acids Res..

The RCSB protein data bank: integrative view of protein, gene and 3D structural information

David S. Goodsell, Andreas Prlic, Zukang Feng, 2016, Nucleic Acids Res..

Automated evaluation of quaternary structures from protein crystals

Jose M. Duarte, Spencer Bliven, Aleix Lafita, 2017 .

MMTF - an efficient file format for the transmission, visualization, and analysis of macromolecular structures

Anthony R. Bradley, Jose M. Duarte, Andreas Prlić, 2017 .

Automated evaluation of quaternary structures from protein crystals

Jose M. Duarte, Spencer Bliven, Aleix Lafita, 2017, bioRxiv.

Web-based molecular graphics for large complexes

Andreas Prlic, Anthony R. Bradley, Jose M. Duarte, 2016, Web3D.

Real time structural search of the Protein Data Bank

Stephen K. Burley, Jose M. Duarte, Dmytro Guzenko, 2020, PLoS Comput. Biol..

Scalable 3D molecular graphics on the web

Jose M. Duarte, Andreas Prlić, Alexander S. Rose, 2016 .

Preparing for the 3D data deluge: real time structural search at the scale of the PDB and beyond

Stephen K. Burley, Jose M. Duarte, Dmytro Guzenko, 2019 .

PDBWiki: added value through community annotation of the Protein Data Bank

Dan M. Bolser, Michael Lappe, Jong Bhak, 2010, Database J. Biol. Databases Curation.

MMTF—An efficient file format for the transmission, visualization, and analysis of macromolecular structures

Andreas Prlic, Anthony R. Bradley, Antonín Pavelka, 2017, PLoS Comput. Biol..

Protein interface classification by evolutionary analysis

Adam Srebniak, Jose M. Duarte, Guido Capitani, 2012, BMC Bioinformatics.

Optimal contact definition for reconstruction of Contact Maps

Michael Lappe, Jose M. Duarte, Ioannis Filippis, 2010, BMC Bioinformatics.

Compressive structural bioinformatics: High efficiency 3D structure compression

Jose M. Duarte, Andreas Prlić, Alexander S. Rose, 2016 .

Defining an Essence of Structure Determining Residue Contacts in Proteins

Michael Lappe, Jose M. Duarte, Ioannis Filippis, 2009, PLoS Comput. Biol..

Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts

Jose M. Duarte, Spencer Bliven, Guido Capitani, 2015, Bioinform..

Scalable analysis and visualization of large 3D macromolecular complexes

Jose M. Duarte, Andreas Prlić, Alexander S. Rose, 2016 .

CMView: Interactive contact map visualization and analysis

Michael Lappe, Juliane Dinse, Jose M. Duarte, 2011, Bioinform..

NGL viewer: web‐based molecular graphics for large complexes

Andreas Prlic, Anthony R. Bradley, Jose M. Duarte, 2018, Bioinform..

RCSB Protein Data Bank 1D tools and services

John D. Westbrook, Stephen K. Burley, Jose M. Duarte, 2020, Bioinform..

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

David S. Goodsell, Zukang Feng, John D. Westbrook, 2020, Nucleic Acids Res..

Designing evolvable libraries using multi-body potentials.

Michael Lappe, Ganesh Bagler, Jose M. Duarte, 2009, Current opinion in biotechnology.

A PDB-wide, evolution-based assessment of protein–protein interfaces

Jose M. Duarte, Spencer Bliven, Guido Capitani, 2014, BMC Structural Biology.

An analysis of oligomerization interfaces in transmembrane proteins

Jose M. Duarte, Guido Capitani, Nikhil Biyani, 2013, BMC Structural Biology.

Small angle X‐ray scattering‐assisted protein structure prediction in CASP13 and emergence of solution structure differences

John A Tainer, Jose M. Duarte, Krzysztof Fidelis, 2019, Proteins.

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework

Julia Koehler Leman, Jose M. Duarte, David L. Masica, 2017 .

The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors

Jose M. Duarte, H. Lehrach, M. Lappe, 2011, Molecular Cancer.

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

Zukang Feng, Helen M Berman, Cole H. Christie, 2017, Protein science : a publication of the Protein Society.

RCSB Protein Data Bank: Views of structural biology for basic and applied research

John D. Westbrook, Helen M. Berman, Stephen K. Burley, 2016 .

Automated finding of assemblies in protein crystal structures

Jose M. Duarte, Spencer Bliven, Aleix Lafita, 2016 .

Assessment of protein assembly prediction in CASP13

Jose M. Duarte, Dmytro Guzenko, Andriy Kryshtafovych, 2019, Proteins.

Exploring protein symmetry at the RCSB Protein Data Bank

Jose M. Duarte, D. Goodsell, S. Burley, 2022, Emerging topics in life sciences.

RCSB Protein Data Bank: Enabling biomedical research and drug discovery

Chenghua Shao, Jose M. Duarte, Christine Zardecki, 2019, Protein science : a publication of the Protein Society.

Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students

Jose M. Duarte, A. Sali, H. Berman, 2022, Biomolecules.

RCSB Protein Data Bank 1D3D module: displaying positional features on macromolecular assemblies

Jose M. Duarte, S. Burley, J. Segura, 2022, Bioinform..

RCSB Protein Data bank: Tools for visualizing and understanding biological macromolecules in 3D

Jose M. Duarte, Ben M. Webb, Sai J. Ganesan, 2022, Protein science : a publication of the Protein Society.

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

Jose M. Duarte, Rachel Kramer Green, Ben M. Webb, 2022, Nucleic Acids Res..

Protein Data Bank: the single global archive for 3D macromolecular structure data

Cole H. Christie, Jose M. Duarte, Rachel Kramer Green, 2018, Nucleic acids research.

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework

Elizabeth Brunk, Binghuang Cai, Yang Zhang, 2017, Genome Medicine.

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

Jose M. Duarte, Sai J. Ganesan, A. Sali, 2021, Protein science : a publication of the Protein Society.

RCSB Protein Data Bank: Sustaining a living digital data resource that enables breakthroughs in scientific research and biomedical education

Zukang Feng, John D. Westbrook, Helen M. Berman, 2017, Protein science : a publication of the Protein Society.

RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive

Jose M. Duarte, Alexander S. Rose, J. Westbrook, 2020, Journal of molecular biology.

RCSB Protein Data Bank: Sustaining A Living Digital Data Resource That Enables Breakthroughs In Scientific Research And Biomedical Education

Cole H. Christie, Jose M. Duarte, H. Berman, 2018, Biophysical Journal.

Simplified quality assessment for small-molecule ligands in the Protein Data Bank.

Jose M. Duarte, J. Westbrook, S. Burley, 2022, Structure.

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

Jose M. Duarte, J. Westbrook, S. Burley, 2021, Bioinform..

Towards an efficient compression of 3D coordinates of macromolecular structures

Jose M. Duarte, Andreas Prlić, Alexander S. Rose, 2017, PloS one.

Protein interface classification by evolutionary analysis

Jose M. Duarte, Martin A. Schärer, G. Capitani, 2012, BMC Bioinformatics.

Investigation of protein quaternary structure via stoichiometry and symmetry ınformation

Jose M. Duarte, Andreas Prlić, Gokmen Zararsiz, 2018, PloS one.

BioJava 5: A community driven open-source bioinformatics library

Paolo Pavan, Matt Larson, Anthony Bradley, 2019, PLoS Comput. Biol..

RCSB Protein Data Bank: integrated searching and efficient access to macromolecular structure data from the PDB archive

Jose M. Duarte, Alexander S. Rose, J. Westbrook, 2021, Acta Crystallographica Section A Foundations and Advances.

Protein interface classification by evolutionary analysis

Jose M. Duarte, Martin A. Schärer, G. Capitani, 2012, BMC Bioinformatics.

RCSB Protein Data Bank: Efficient Searching and Simultaneous Access to One Million Computed Structure Moddels Alongside the PDB Structures Enabled by Architectural Advances.

Jose M. Duarte, J. Westbrook, S. Burley, 2023, Journal of molecular biology.

Assessment of protein assembly prediction in CASP12

Torsten Schwede, Jose M. Duarte, Andriy Kryshtafovych, 2018, Proteins.

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework

Jose M. Duarte, Sheila M. Reynolds, G. Barton, 2017, Genome Medicine.

Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys

Michael Lappe, Jose M. Duarte, Ioannis Filippis, 2008, BMC Structural Biology.

Quaternary structure evaluation tool for protein assemblies

Stephen K. Burley, Peter W. Rose, Jose M. Duarte, 2017, bioRxiv.