Group Members

Pictures!

PI

Matt Jacobson

UCSF MC 2540

1700 4^th St.

Byers Hall, Room 408E

San Francisco, CA 94158-2330

matt.jacobson-at-ucsf.edu

415-514-9811

415-502-4222 (FAX)

Please note: I rarely answer my office phone and infrequently check messages there, in part due to an increase in sales calls. If you wish to schedule a phone conversation, please reach me first by email.

Administrative Analyst

JoAnne Williams (on temporary leave)

Please contact Lili Li, LiL-at-medsch.ucsf.edu

Research Staff

Chakrapani Kalyanaraman

Associate Research Chemist

Predicting enzyme function; protein-ligand docking

ck-at-cgl.ucsf.edu

Teague Sterling

Computer Systems Administrator

teague-at-blur.compbio.ucsf.edu

Postdoctoral Researchers

Salma Rafi

Allostery and membrane permeability

Lan Hua

Drug discovery for blood diseases

Michael Chimenti (joint with Mark Kelly)

Fragment-based drug discovery

Siegfried Leung

Passive membrane permeability

Elena Dolghih

Blood-brain barrier including P-glycoprotein

Adam Steeves (jointly advised by John Gross and Dave Morgan)

NIH Postdoctoral Fellow

Protein allostery

Suwen Zhou

Enzyme specificity/function prediction

Morena Spreafico

SNF Fellow

Computer-aided antibody design

Frank Wallrapp

Enzyme specificity/function prediction

Katrina Lexa (jointly advised by Michael Fischbach and James Fraser)

NIH Postdoctoral Fellow

Macrocyclic natural products in drug discovery

Lili Peng

Mechanisms of drug action on microtubules

Graduate Students

Monica Tremont

Graduate Group in Biophysics

Multi-scale simulations of microtubules

John Bruning (joint advisor with Robert Fletterick)

PSPG Graduate Program

Boxue Tian

Visiting student, NUI Galway

Predicting enzyme specificity

Current Rotation Students: Sara Calhoun (Biophysics), Diego Garrido Ruiz (Biophysics)

Summer Students: Paulomi Bhattacharya (high school student), Linsey Brier (undergraduate student, SRTP)

Group News

• June 2012: Global Blood Therapeutics (globalbloodtx.com) receives Series A funding from Third Rock Ventures
• January 2012: Matt and his longtime collaborator Scott Lokey (UCSC) are awarded a Johnson&Johnson ‘Bridging the Gap‘ award to help commercialize their technology for engineering orally bioavailable cyclic peptides.
• November 2011: Katrina receives an NIH Postdoctoral Fellowship.
• July 2011: Matt is promoted to Full Professor.
• April 2011: Chris is awarded the Frank Goyan prize (given for a superior thesis in physical chemistry at UCSF), the third member of the Jacobson lab to win this honor. Chris later receives an NIH Postdoctoral Fellowship for his current position at UCSD.
• July 2010: Adam receives an NIH Postdoctoral Fellowship.
• April 2009: Monica is awarded an NSF graduate fellowship.
• December 2008: Chris is awarded a PhRma informatics fellowship.
• 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	Scientist, Illumina
Sergio Wong	Graduate Group in Biophysics	9/02-9/06	trulybored-at-gmail.com	Scientist, Lawrence Livermore National Lab
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 (Cambridge)
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
Francesca Milletti	Visiting student, Università degli Studi di Perugia	1/08-10/08	francesca.milletti-at-gmail.com	Scientist, Roche (Nutley)
Eli Groban	Graduate Group in Biophysics	6/03-12/08	egroban-at-gmail.com	Scientist, Intrexon
Ben Sellers	Graduate Group in Biophysics	6/03-12/08	sellersb-at-gmail.com	Computational chemist, Genentech
Jerome Nilmeier	Graduate Group in Biophysics	6/03-12/08	jnilmeier-at-yahoo.com	Postdoc, LLNL
Arjun Narayanan	Graduate Group in Biophysics	6/04-12/09	arjun.nufc-at-gmail.com	Scientist, Roche (Nutley)
Colin Smith	Graduate Group in Bioinformatics	2005-2011		Postdoc, Max Planck Institute
Chris McClendon	Graduate Group in Biophysics	2005-2011		Postdoc, UCSD

Former rotation students: Kale Kundert (Biophysics, 2011), Catherine Shi (Biophysics, 2011), John Bruning (PSPG, 2010), Geoff Rollins (Biophysics, 2009), Andrew Wiser (CCB, 2009), Henry Lin (Bioinformatics, 2008), 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 undergraduate summer students: Amy Ye (2008 Amgen Scholar, U. Illinois Chicago), Dinah Zaghi and Reina Eisner (2005 and 2006, respectively; both from Stern College, Yeshiva University).

Former student visitors: Daisuke Kuroda (2010; Osaka U.), Jona Mijalkovic (2009-2010; Leiden U.), Alrun Koller (2009; U. Dusseldorf, group of Holger Gohlke), Hod Greeley (2003-2004; visiting graduate student, Columbia University).

Former sabbatical visitors: Pradipta Bandyopadhyay (2008; Jawaharlal Nehru University, New Delhi, India), Evangelos “Vageli” Coutsias (summer 2008; U. New Mexico), Chris Oostenbrink (summer 2006; currently at U. Natural Resources and Life Sciences, Vienna),