User:Russell C. Goodman

Contact Info



 * Russell C. Goodman
 * University of California, San Francisco
 * Integrative Program in Quantitative Biology (iPQB)
 * Russell.Goodman@ucsf.edu
 * Goodman.Russell.C@gmail.com

Intentions of Wiki
I've joined OWW to make my work on predicting binding sites on intrinsically disordered proteins (IDPs) open to the biological community.

SeqCom and IUPattern Report
This is a PDF version of our poster presented at the 55th Annual Biophysical Society Meeting: This report summarizes the performance of SeqCom, IUPattern, and IUPatternC on the IDPs in our database:
 * [[image:Poster1.pdf|alt text]]
 * [[image:Paper_SP11.pdf|alt text]]

SeqCom
SeqCom is our primitive sequence composition algorithm that uses statistical parameters to make predictions on probable binding sites on nucleic acid binding intrinsically unstructured proteins. Refer to Paper_SP11.pdf in the reports section for a more detailed description of the algorithm and its performance. Refer to the instructions section for information on using SeqCom.
 * [[Image:SeqCom.txt|alt text]]

IUPattern
IUPattern is an sequence composition algorithm that uses statistical parameters to make predictions on probable binding sites on nucleic acid binding intrinsically unstructured proteins. As opposed to SeqCom, IUPattern has constraints in its algorithm that require patterns of secondary structure formation or straight chain binding to be present before the final binding site predictions are produced. IUPattern is now programmed to parse FASTA files! Refer to Paper_SP11.pdf in the reports section for a more detailed description of the algorithm and its performance.
 * [[Image:IUPattern.txt|alt text]]

IUPatternC
The source code of IUPatternC is posted! Preliminary analysis suggests that IUPatternC decreases false positive prediction; however, there is some compromise on true positive predictions compared to IUPattern. The IUPattern instructions will work for IUPatternC. Refer to Paper_SP11.pdf in the reports section for a more detailed description of the algorithm and its performance.
 * [[Image:IUPatternC.txt|alt text]]

Instructions
These files contain instructions for compiling and running the IDP applications and interpreting the output files of the applications.

SeqCom
Instructions for the use of SeqCom:
 * [[Image:SeqCom_Instructions.pdf|alt text]]

IUPattern and IUPatternC
Instructions for the use of IUPattern:
 * [[Image:IUPattern_Instructions.pdf|alt text]]

Education
B.S., Le Moyne College, Biochemistry, summa cum laude (2011).

Le Moyne College

 * Undergraduate Thesis Title: Prediction of binding sites on nucleic acid binding intrinsically disordered proteins (September 2008-)
 * Mentor: Theresa L. Beaty, Ph.D.

Massachusetts Institute of Technology

 * Oligomerization State and Orientation of Synzips for Molecular Engineering (June 2010-August 2010)
 * Mentor: Amy E. Keating, Ph.D.
 * Supervisor: Evan Thompson, Ph.D.

University of Rochester

 * Effect of Coaxial Stacking of Helices on RNA Secondary Structure Prediction (June 2009-August 2009)
 * Mentor: David H. Mathews, M.D., Ph.D.

Research Interests
My research interests are in the area of protein structure prediction and design.

Publications and Presentations

 * Goodman, R. C., Beaty, T. L. 2011. Prediction of Binding Sites on Intrinsically Disordered Proteins. Presented at 55th Annual Biophysical Society Meeting, Baltimore, MD, March 6, 2011.
 * Goodman, R. C., Thompson E., Keating A. E. 2010. Oligomerization State and Orientation of Synzips for Molecular Engineering. Presented at 25th Annual MIT Summer Research Program and Broad Institute Poster Session, Cambridge, MA, August 5, 2010.
 * Goodman, R. C., Xu, Z., Mathews, D. H. 2010. Effect of coaxial stacking of helices on RNA secondary structure prediction. Presented at the 2010 National ACS Meeting, San Francisco, CA, March 23, 2010.
 * Goodman, R. C., Beaty T. L. 2010. Predication of binding sites on nucleic acid binding intrinsically unstructured proteins. Presented at 2010 WNY ACS Undergraduate Research Symposium, Niagara Falls, NY, March 6, 2010.
 * Goodman, R. C., Xu, Z., Mathews, D. H. 2009. Effect of coaxial stacking of helices on RNA secondary structure prediction. Presented at 2009 Summer Scholars Poster Session, Rochester, NY, August 6, 2009.

Useful links

 * Introductory tutorial
 * OpenWetWare help pages