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....
- 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...
- 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...
- 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...