John H Morris
Affiliation: University of California
- structureViz: linking Cytoscape and UCSF ChimeraJohn H Morris
Department of Pharmaceutical Chemistry, University of California, San Francisco, USA
Bioinformatics 23:2345-7. 2007..This interface uses a tree-based paradigm to allow users to select and affect the display of models, chains and residues, mostly through the use of context menus...
- clusterMaker: a multi-algorithm clustering plugin for CytoscapeJohn H Morris
Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA
BMC Bioinformatics 12:436. 2011....
- Protein network prediction and topological analysis in Leishmania major as a tool for drug target selectionAndrés F Flórez
Programa de Estudio y Control de Enfermedades Tropicales PECET, Universidad de Antioquia, Calle 62 No 52 59, Lab 632, Medellin, Colombia
BMC Bioinformatics 11:484. 2010..We have taken a computational approach to the detection of new drug targets, which may become an effective strategy for the discovery of new drugs for this tropical disease...
- Improving the quality of protein similarity network clustering algorithms using the network edge weight distributionLeonard Apeltsin
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
Bioinformatics 27:326-33. 2011..We investigate an important aspect of network construction used in analyzing protein superfamilies and present a heuristic approach for improving the performance of several algorithms...
- Computational tools for the interactive exploration of proteomic and structural dataJohn H Morris
Resource for Biocomputing, Visualization, and Informatics, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158 2517, USA
Mol Cell Proteomics 9:1703-15. 2010..We briefly describe several relevant tools, and then, using three scenarios, we present in depth two tools for the integrated exploration of proteomics and structural data...
- The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouseAlex S Nord
University of California San Francisco, 600 16th Street, San Francisco, CA 94143 2240, USA
Nucleic Acids Res 34:D642-8. 2006....
- Using sequence similarity networks for visualization of relationships across diverse protein superfamiliesHolly J Atkinson
Graduate Program in Biological and Medical Informatics, University of California San Francisco, San Francisco, California, United States of America
PLoS ONE 4:e4345. 2009..As a broadly accessible and effective tool for the exploration of protein superfamilies, sequence similarity networks show great potential for generating testable hypotheses about protein structure-function relationships...
- Leveraging enzyme structure-function relationships for functional inference and experimental design: the structure-function linkage databaseScott C H Pegg
Department of Biopharmaceutical Sciences, University of California, San Francisco, 1700 Fourth Street, San Francisco, California 94143 2250, USA
Biochemistry 45:2545-55. 2006..The SFLD is freely accessible at http://sfld.rbvi.ucsf.edu...
- From Structure to Systems: High-Resolution, Quantitative Genetic Analysis of RNA Polymerase IIHannes Braberg
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA California Institute for Quantitative Biosciences, QB3, San Francisco, CA 94158, USA
Cell 154:775-88. 2013..The pE-MAP approach provides a powerful strategy to understand other multifunctional machines at amino acid resolution. ..
- Global landscape of HIV-human protein complexesStefanie Jäger
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94158, USA
Nature 481:365-70. 2012..This data set facilitates a more comprehensive and detailed understanding of how the host machinery is manipulated during the course of HIV infection...