Group Members

Pictures!

PI

Matt Jacobson

UCSF MC 2240

Genentech Hall Room N472C

600 16^th Street

San Francisco, CA 94158-2517

matt.jacobson@ucsf.edu

415-514-9811

415-502-4222 (FAX)

Administrative Analyst

JoAnne Williams

415-476-8679

joanne-at-maxwell.ucsf.edu

Research Staff

Chakrapani Kalyanaraman

Assistant Research Chemist

ck-at-cgl.ucsf.edu

Pascal Wassam

Computer Systems Administrator

415-514-4403

pascal-at-blur.compbio.ucsf.edu

Postdoctoral Researchers

Salma Rafi

sbrafi-at-gmail.com

Graduate Students

Eli Groban (joint with Chris Voigt)

Graduate Group in Biophysics

egroban-at-gmail.com

Jerome Nilmeier

Graduate Group in Biophysics

jpnil-at-hotmail.com

Ben Sellers

Graduate Group in Biophysics

sellersb-at-gmail.com

Arjun Narayanan

Graduate Group in Biophysics

arjun.nufc-at-gmail.com

Colin Smith (joint with Tanja Kortemme)

Biological and Medical Informatics

colin.smith-at-ucsf.edu

Christopher McClendon (joint with Jim Wells)

Graduate Group in Biophysics

Christopher.Mcclendon-at-ucsf.edu

Monica Tremont

Graduate Group in Biophysics

monica.tremont-at-gmail.com

Current Visitors

Francesca Milletti

Università degli Studi di Perugia (Cruciani group)

francesca.milletti-at-gmail.com

Amy Ye

University of Illinois at Chicago (undergraduate)

Amgen Scholar, UCSF Summer Research Training Program

Pradipta Bandyopadhyay

Associate Professor

Jawaharlal Nehru University, New Delhi, India

Evangelos (Vageli) Coutsias

Professor, Department of Mathematics and Statistics

University of New Mexico

Group News

• July 2008: Matt becomes director of the Graduate Group in Biophysics.
• June 2008: Chris is awarded a CRCC Fellowship for 2008-2009.
• June 2008: Monica is awarded a Chancellor’s Fellowship for 2008-2009.
• April 2008: Eli wins the Frank Goyan award for 2007 (given for a superior thesis in physical chemistry at UCSF).
• November 2007: Matt becomes an Associate Editor at PLoS Computational Biology
• April 2007: Sergio wins the Frank Goyan award for 2006 (given for a superior thesis in physical chemistry at UCSF).
• March 2007: Matt gets tenure!
• March 2007: Colin is offered a Department of Energy Computational Science Graduate Fellowship, NSF fellowship, and NDSEG fellowship.
• February 2007: Colin is selected as one of only two Genentech Scholars at the graduate level for 2007.
• November 2006: Niu accepts a faculty position at the National Institute of Biological Sciences, Beijing.
• April 2006: Nima is awarded a prestigious National Defense Science and Engineering Graduate Fellowship.
• April 2006: CK and Kat’s paper “Virtual screening against highly charged active sites: Identifying substrates of alpha-beta barrel enzymes”, is cited as one of the top 20 “most accessed” articles in Biochemistry during 2005.
• November 2005: The Sandler Program awards our group, along with Diane Barber and Mark Kelly, an Integrative Research Award for our collaborative project entitled “Regulation of Proteins and Cell Processes by Small Changes in pH”.
• June 2005: Sergio is awarded a UCSF President’s Dissertation Year Fellowship for 2005-2006.
• February 2005: Our group is invited to submit a paper describing our participation in the McMaster Data Mining and Docking Competition. This work was done by Kat, with assistance from CK.
• August 2004: Our work on antibodies is funded by an Opportunity Award from the Sandler Program in Basic Sciences. Thank you to Ben and Jerome for all your hard work on this project.
• August 2004: Ben is awarded a Genentech Fellowship for the upcoming year.
• July 2004: Eli is awarded a UCSF Program in Quantitative Biology Burroughs Wellcome Fellowship, and becomes a joint student with Chris Voigt.
• June 2004: A Program Project grant headed by John Gerlt (UIUC) entitled “Deciphering Enzyme Specificity” is funded. We are part of the computational project, headed by Patsy Babbitt.
• Februrary 2004: Matt is selected for the Alfred P. Sloan Fellowship.
• January 2004: Matt is selected for the NSF CAREER award. This funding will support the phosphorylation project.
• June 2003: Protein Local Optimization Program is licensed by UCSF and Columbia to Schrödinger, Inc. for commercial distribution. Schrödinger markets the code as part of the PRIME (Protein Integrated Modeling Environment) package and distributes first beta release.
• June 2003: Sergio is awarded a UCSF Program in Quantitative Biology Burroughs Wellcome Fellowship.
• May 2003: Ilya is awarded a Sloan/DOE Postdoctoral Fellowship in Computational Molecular Biology/Bioinformatics.
• April 2003: Jim McKerrow's NIH Biodefense Program Project Grant, "Targeting Cysteine Proteases of Category B Pathogens", is funded. Our group and Tack Kuntz's group will jointly comprise the "Computational Core".
• March 2003: Katarzyna is awarded an NSF Postdoctoral Fellowship in Interdisciplinary Informatics.

Former Group Members

Who	What	Dates	Current Email	Current Position
Ilya Chorny	Sloan Postdoctoral Fellow	9/03-6/05	ichorny-at-gmail.com	Stroud Lab, UCSF Simprota Inc.
Sergio Wong	Graduate Group in Biophysics	9/02-6/06	trulybored-at-gmail.com	Postdoc, McCammon group, UCSD
Katarzyna Bernacki	NSF Postdoctoral Fellow	11/02-6/06	kasia.bernacki-at-gmail.com
Laura Dominguez	Visiting student, Specialist	4/06-1/07	lauraok-at-gmail.com	PhD student, UNAM
Gabriela Barreiro	Postdoctoral researcher	2/05-9/06	gabriela.barreiro-at-gmail.com	Pfizer (Groton)
Niu Huang	Postdoctoral researcher	10/03-9/06	huangniu-at-nibs.ac.cn	National Institute of Biological Sciences (Beijing)
Nima Fayazmanesh	MSTP/Graduate Group in Biophysics	9/03-3/08	nimafayazmanesh-at-gmail.com	UCSF Medical School

Former rotation students: Kris Kuchenbecker (Biophysics, 2007), Rebeca Choy (Biophysics, 2006), Jeremy Philips (BMI, 2006), Stephen Floor (Biophysics, 2006), Hesper Rego (Biophysics, 2006), Dan Mandell (BMI, 2005), David Lomelin (BMI, 2004), Brian Tuch (BMI, 2003), Chris Farady (Biophysics, 2002).

Former summer students: Dinah Zaghi, Reina Eisner (both from Stern College, Yeshiva University)

Former visitors: Chris Oostenbrink (sabbatical visitor, summer 2006), Hod Greeley (visiting graduate student, Columbia University)