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Author Details

Peter W Rose
University of California
1999
41
23
PMIDPaper TitleJournal TitlePublished Year
35394655The Pfizer Crystal Structure Database: An essential tool for structure-based design at Pfizer.J Comput Chem2022
33983959Ten simple rules to cultivate transdisciplinary collaboration in data science.PLoS Comput Biol2021
30357411RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy.Nucleic Acids Res2019
31744546The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.Genome Biol2019
31344036Ten simple rules for writing and sharing computational analyses in Jupyter Notebooks.PLoS Comput Biol2019
31009453Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm.PLoS Comput Biol2019
30735498BioJava 5: A community driven open-source bioinformatics library.PLoS Comput Biol2019
29457794Recon3D enables a three-dimensional view of gene variation in human metabolism.Nat Biotechnol2018
29864163Investigation of protein quaternary structure via stoichiometry and symmetry information.PLoS One2018
29850778NGL viewer: web-based molecular graphics for large complexes.Bioinformatics2018
27995514The need for scientific software engineering in the pharmaceutical industry.J Comput Aided Mol Des2017
28362865Towards an efficient compression of 3D coordinates of macromolecular structures.PLoS One2017
28334105BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank.Bioinformatics2017
28296894Impact of genetic variation on three dimensional structure and function of proteins.PLoS One2017
29254494Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.Genome Med2017
28574982MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures.PLoS Comput Biol2017
27794042The RCSB protein data bank: integrative view of protein, gene and 3D structural information.Nucleic Acids Res2017
27551105Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank.Bioinformatics2016
25183487RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank.Bioinformatics2015
26317409Citing a Data Repository: A Case Study of the Protein Data Bank.PLoS One2015
25428375The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.Nucleic Acids Res2015
24681267Systematic detection of internal symmetry in proteins using CE-Symm.J Mol Biol2014
23337870Trendspotting in the Protein Data Bank.FEBS Lett2013
23193259The RCSB Protein Data Bank: new resources for research and education.Nucleic Acids Res2013
22877863BioJava: an open-source framework for bioinformatics in 2012.Bioinformatics2012
21036868The RCSB Protein Data Bank: redesigned web site and web services.Nucleic Acids Res2011
21382834Quality assurance for the query and distribution systems of the RCSB Protein Data Bank.Database (Oxford)2011
20429930Integration of open access literature into the RCSB Protein Data Bank using BioLit.BMC Bioinformatics2010
20937596Pre-calculated protein structure alignments at the RCSB PDB website.Bioinformatics2010
20195550Will widgets and semantic tagging change computational biology?PLoS Comput Biol2010
15911263Design, synthesis, and biological evaluation of novel human 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP) substrates.Bioorg Med Chem Lett2005
12697905Simulating disorder-order transitions in molecular recognition of unstructured proteins: where folding meets binding.Proc Natl Acad Sci U S A2003
14521419Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors. 8. Pharmacological optimization of orally bioavailable 2-pyridone-containing peptidomimetics.J Med Chem2003
14517972Computational detection of the binding-site hot spot at the remodeled human growth hormone-receptor interface.Proteins2003
11754580Hierarchy of simulation models in predicting structure and energetics of the Src SH2 domain binding to tyrosyl phosphopeptides.J Med Chem2002
12112677Monte Carlo simulations of the peptide recognition at the consensus binding site of the constant fragment of human immunoglobulin G: the energy landscape analysis of a hot spot at the intermolecular interface.Proteins2002
11959497Complexity and simplicity of ligand-macromolecule interactions: the energy landscape perspective.Curr Opin Struct Biol2002
11746693Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes: structural analysis of the peptide complexes with SH2 domains.Proteins2001
11131967Deciphering common failures in molecular docking of ligand-protein complexes.J Comput Aided Mol Des2000
10611647Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions.J Mol Recognit1999
10380216Thermodynamics and kinetics of ligand-protein binding studied with the weighted histogram analysis method and simulated annealing.Pac Symp Biocomput1999
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Collaborators

Andreas Prli??
University of California
Co-authored papers 24
Philip E Bourne
University of Virginia
Co-authored papers 12
Stephen K Burley
The State University of New Jersey
Co-authored papers 9
Chunxiao Bi
University of California San Diego
Co-authored papers 9
Jose M Duarte
University of California San Diego
Co-authored papers 8
Helen M Berman
The State University of New Jersey
Co-authored papers 8
Christine Zardecki
The State University of New Jersey
Co-authored papers 7
Jasmine Young
The State University of New Jersey
Co-authored papers 7
Cole H Christie
University of California
Co-authored papers 6
Alexander S Rose
University of California San Diego
Co-authored papers 5
John D Westbrook
The State University of New Jersey
Co-authored papers 5
Shuchismita Dutta
The State University of New Jersey
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David S Goodsell
The State University of New Jersey
Co-authored papers 5
Rachel Kramer Green
The State University of New Jersey
Co-authored papers 4
Tami Marrone
Co-authored papers 4
Brian P Hudson
The State University of New Jersey
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Ezra Peisach
The State University of New Jersey
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Chenghua Shao
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Co-authored papers 3
Michael Heuer
University of California Berkeley
Co-authored papers 3
Huanwang Yang
The State University of New Jersey
Co-authored papers 3
Jianjiong Gao
Memorial Sloan Kettering Cancer Center
Co-authored papers 3
Luigi Di Costanzo
University of Naples Federico II
Co-authored papers 3
Maria Voigt
The State University of New Jersey
Co-authored papers 3
Robert Lowe
The State University of New Jersey
Co-authored papers 2
Chris Randle
University of California
Co-authored papers 2
Sean D Mooney
University of Washington
Co-authored papers 2
Dmytro Guzenko
University of California
Co-authored papers 2
Yi-Ping Tao
The State University of New Jersey
Co-authored papers 2
Sutapa Ghosh
The State University of New Jersey
Co-authored papers 2
Timothy Bergquist
University of Washington School of Medicine
Co-authored papers 2
Release 1.2