Philip E. Bourne
Orcid: 0000-0002-7618-7292Affiliations:
- San Diego Supercomputer Center, USA
According to our database1,
Philip E. Bourne
authored at least 184 papers
between 1994 and 2024.
Collaborative distances:
Collaborative distances:
Timeline
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Online presence:
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on zbmath.org
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on twitter.com
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on orcid.org
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on id.loc.gov
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on sdsc.edu
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on isni.org
On csauthors.net:
Bibliography
2024
Prop3D: A flexible, Python-based platform for machine learning with protein structural properties and biophysical data.
BMC Bioinform., December, 2024
2023
PLoS Comput. Biol., December, 2023
Big Data Soc., July, 2023
Analysis of KRAS-Ligand Interaction Modes and Flexibilities Reveals the Binding Characteristics.
J. Chem. Inf. Model., February, 2023
End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins.
PLoS Comput. Biol., January, 2023
CoRR, 2023
2022
PLoS Comput. Biol., 2022
Ten simple rules for using entrepreneurship skills to improve research careers and culture.
PLoS Comput. Biol., 2022
PLoS Comput. Biol., 2022
Correction to "Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants".
J. Chem. Inf. Model., 2022
2021
PLoS Comput. Biol., 2021
J. Am. Medical Informatics Assoc., 2021
Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology.
CoRR, 2021
2020
PLoS Comput. Biol., 2020
2019
PLoS Comput. Biol., 2019
Analyzing the symmetrical arrangement of structural repeats in proteins with CE-Symm.
PLoS Comput. Biol., 2019
Structural Insights into Characterizing Binding Sites in Epidermal Growth Factor Receptor Kinase Mutants.
J. Chem. Inf. Model., 2019
Natural language processing of symptoms documented in free-text narratives of electronic health records: a systematic review.
J. Am. Medical Informatics Assoc., 2019
A systematic review of natural language processing and text mining of symptoms from electronic patient-authored text data.
Int. J. Medical Informatics, 2019
2018
PLoS Comput. Biol., 2018
2017
PLoS Comput. Biol., 2017
BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank.
Bioinform., 2017
2016
Drug repurposing to target Ebola virus replication and virulence using structural systems pharmacology.
BMC Bioinform., 2016
2015
PLoS Comput. Biol., 2015
Ten Years of <i>PLoS<sup>‡</sup> Computational Biology: </i> A Decade of Appreciation and Innovation.
PLoS Comput. Biol., 2015
PLoS Comput. Biol., 2015
The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.
Nucleic Acids Res., 2015
J. Am. Medical Informatics Assoc., 2015
Editor's Choice: Achievements and challenges in structural bioinformatics and computational biophysics.
Bioinform., 2015
RCSB PDB <i>Mobile</i>: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank.
Bioinform., 2015
Bioinform., 2015
Proceedings of the 2015 IEEE International Conference on Bioinformatics and Biomedicine, 2015
2014
Towards Structural Systems Pharmacology to Study Complex Diseases and Personalized Medicine.
PLoS Comput. Biol., 2014
PLoS Comput. Biol., 2014
Anti-Infectious Drug Repurposing Using an Integrated Chemical Genomics and Structural Systems Biology Approach.
Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014
2013
PLoS Comput. Biol., 2013
PLoS Comput. Biol., 2013
Nucleic Acids Res., 2013
Concurr. Comput. Pract. Exp., 2013
BMC Syst. Biol., 2013
Proceedings of the 9th International Symposium on Open Collaboration, Hong Kong, China, August 05, 2013
2012
PLoS Comput. Biol., 2012
Nucleic Acids Res., 2012
An integrated workflow for proteome-wide off-target identification and polypharmacology drug design.
Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012
2011
Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir.
PLoS Comput. Biol., 2011
PLoS Comput. Biol., 2011
PLoS Comput. Biol., 2011
Nucleic Acids Res., 2011
Nucleic Acids Res., 2011
Nucleic Acids Res., 2011
Correction to "A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing".
J. Chem. Inf. Model., 2011
A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing.
J. Chem. Inf. Model., 2011
Improving The Future of Research Communications and e-Scholarship (Dagstuhl Perspectives Workshop 11331).
Dagstuhl Manifestos, 2011
Comput. Phys. Commun., 2011
Quality assurance for the query and distribution systems of the RCSB Protein Data Bank.
Database J. Biol. Databases Curation, 2011
2010
The <i>Mycobacterium tuberculosis</i> Drugome and Its Polypharmacological Implications.
PLoS Comput. Biol., 2010
A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology.
PLoS Comput. Biol., 2010
PLoS Comput. Biol., 2010
Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model.
PLoS Comput. Biol., 2010
PLoS Comput. Biol., 2010
SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison.
Nucleic Acids Res., 2010
BMC Bioinform., 2010
BMC Bioinform., 2010
dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment.
BMC Bioinform., 2010
Bioinform., 2010
2009
Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors.
PLoS Comput. Biol., 2009
PLoS Comput. Biol., 2009
Drug Discovery Using Chemical Systems Biology: Repositioning the Safe Medicine Comtan to Treat Multi-Drug and Extensively Drug Resistant Tuberculosis.
PLoS Comput. Biol., 2009
A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery.
Bioinform., 2009
2008
PLoS Comput. Biol., 2008
Nucleic Acids Res., 2008
BMC Bioinform., 2008
Intrinsic Evaluation of Text Mining Tools May Not Predict Performance on Realistic Tasks.
Proceedings of the Biocomputing 2008, 2008
2007
In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators.
PLoS Comput. Biol., 2007
PLoS Comput. Biol., 2007
PLoS Comput. Biol., 2007
A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites.
BMC Bioinform., 2007
Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2.
BMC Bioinform., 2007
BMC Bioinform., 2007
2006
PLoS Comput. Biol., 2006
PLoS Comput. Biol., 2006
Application of protein structure alignments to iterated hidden Markov model protocols for structure prediction.
BMC Bioinform., 2006
Proceedings of the Pattern Recognition in Bioinformatics, International Workshop, 2006
Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006
2005
Functional Coverage of the Human Genome by Existing Structures, Structural Genomics Targets, and Homology Models.
PLoS Comput. Biol., 2005
PLoS Comput. Biol., 2005
PLoS Comput. Biol., 2005
PLoS Comput. Biol., 2005
The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema.
Nucleic Acids Res., 2005
The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications.
BMC Bioinform., 2005
Introduction to Informatics Approaches in Structural Genomics: Modeling and Representation of Function from Macromolecular STructure.
Proceedings of the Biocomputing 2005, 2005
2004
New Gener. Comput., 2004
Nucleic Acids Res., 2004
A New Scoring Function and Associated Statistical Significance for Structure Alignment by CE.
J. Comput. Biol., 2004
Statistical and Visual Morph Movie Analysis of Crystallographic Mutant Selection Bias in Protein Mutation Resource Data.
J. Bioinform. Comput. Biol., 2004
Bioinform., 2004
The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures.
Proceedings of the Biocomputing 2004, 2004
Grid Portal Interface for Interactive Use and Monitoring of High-Throughput Proteome Annotation.
Proceedings of the Grid Computing in Life Science, 2004
Proceedings of the Grid Computing in Life Science, 2004
Proceedings of the Second Asia-Pacific Bioinformatics Conference (APBC 2004), 2004
2003
Parallel Processing on Large Redudant Biological Data Sets: Protein Structures Classification with CEPAR.
Proceedings of the Parallel Computing: Software Technology, 2003
Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference, 2003
2002
An ontology driven architecture for derived representations of macromolecular structure.
Bioinform., 2002
Building an automated classification of DNA-binding protein domains.
Proceedings of the European Conference on Computational Biology (ECCB 2002), 2002
2001
A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm.
Nucleic Acids Res., 2001
A New Algorithm for the Alignment of Multiple Protein Structures Using Monte Carlo Optimization.
Proceedings of the 6th Pacific Symposium on Biocomputing, 2001
2000
1999
Bioinform., 1999
Developing Protein Documentaries and Other Multimedia Presentations for Molecular Biology.
Proceedings of the 4th Pacific Symposium on Biocomputing, 1999
1997
Comput. Appl. Biosci., 1997
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997
1995
Design and use of a software framework to obtain information derived from macromolecular structure data.
Proceedings of the 28th Annual Hawaii International Conference on System Sciences (HICSS-28), 1995
1994
An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA.
Comput. Appl. Biosci., 1994
Comput. Appl. Biosci., 1994
Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994