Kufareva group

Research overview

The long-standing goal of our work is to elucidate the structural, molecular, and architectural principles of mammalian cell responses to stimuli and drugs. We approach this challenge at multiple levels, from atomic-resolution molecular interactions to the level of cellular systems, using methods and tools of trans-scale computational biology. 

At the atomic resolution level, we develop methods for accurate computational prediction of transient interactions of proteins and chemicals with conformationally variable protein interfaces, and apply these approaches to important cellular targets. This is complemented by experimental work aimed at identification of bioactive molecules, target characterization and assay development. 

At the systems level, we work towards understanding the architectural principles that govern intracellular signal transduction networks. Inspired by the philosophy of "understanding-by-building", we seek to contribute to the construction of a predictive in silico cell. This challenging task relies on synergistic efforts of experimental, computational, systems, and structural biologists - the network of our talented collaborators in and outside UC San Diego.

Contact information

Irina Kufareva, Ph.D.

Associate Adjunct Professor

Skaggs School of Pharmacy and Pharmaceutical Sciences

University of California at San Diego

Pharmaceutical Sciences Building

9255 Pharmacy Lane, MC 0657

La Jolla, CA 92093-0657, USA

Phone: 1-858-822-4163 

Email: ikufareva@health.ucsd.edu 


May 19, 2024

Kudos to Dr. Suchi Roy and Mr. Grant Wadman for presenting their work at the 2024 ASPET symposium in Arlington, VA. 

June 12, 2023

The long awaited article by Willow, about kboolnet (a toolkit for the verification, validation, and visualization of reaction-contingency / rxncon models) is finally published in BMC Bioinformatics - congrats Willow! Please check out the code and documentation online at https://github.com/Kufalab-UCSD/kboolnet.

May 18, 2023

Kudos to Dr. John Dawson for the excellent presentation of his CCR2 SAR work at the Molsoft ICM User Group Meeting (UGM).

April 5, 2023

Welcome our new team member, Grant Wadman!

Feb 22, 2023

A round of applause to Alexis and John for presenting their posters at the 67th Biophysical Society meeting in San Diego. The meeting was a blast and the posters got lots of interest. Stay tuned for the respective published papers.

October 1, 2022

So happy Sofia Endzhievskaya, the new postdoc experimentalist, made it here from London. Welcome Sofia!

July 1, 2022

Welcome John Dawson, a new postdoc in the Kufareva lab, who will be focusing on structure-based drug discovery for CCR2 and other chemokine receptors.

March 31, 2022

The special “GPCR Dock 2021 Results and Analysis” symposium will take place on April 13-14th, 2022, 8pm-0:30am Shanghai time (April 13 5am-9:30am PDT) as part of the annual iHuman Forum. This will be a half-day of GPCR modeling and docking science with a keynote speaker, an address from the organizers, presentation of results and team rankings, overview of the field progress, and talks by the creators of the most accurate models. Looking forward to your participation and please spread the word!

Nov 4, 2021

Happy to announce GPCR Dock 2021, a new round of the community-wide GPCR modeling and docking assessment, organized by UC San Diego and iHuman Institute of ShanghaiTech: https://gpcrdock2021.org/ Please register early and make sure to tell your friends and colleagues!

Sep 15, 2021

Welcome Rezvan "Leila" Chitsazi, a new postdoc in the lab. Leila will be working on projects related to structural pharmacology of chemokine and other G protein coupled receptors.

May 24, 2021

An official welcome to the two new lab members: Julie Resnick (a junior at UCSD) and Beatrice Acot (a junior at the Eastlake High School in Chula Vista, CA). Both Beatrice and Julie are starting in the lab as volunteer interns.

April 14, 2021

Kirti Chahal has successfully passed her examination/defended her thesis at the Guru Jambheshwar University of Science and Technology, Hisar, India. She is now officially a PhD. Please congratulate the new Dr. Kirti! And many thanks to all the lab members and collaborators for their continuing support; this amazing achievement would not be possible without you all!

Feb 8, 2021

Welcome Dmytro "Dima" Ilnytskyy, a senior from Poway High School, who has joined the lab as a volunteer intern!

July 14, 2020

The paper by Bryan Stephens, about the functional anatomy of the CXCR4-CXCL12 complex, has been published in Science Signaling. Furthermore, together with Tony's PLOS Biology study, it was featured in the UC San Diego Health Sciences blog post. This is another collaborative study with the Handel lab. Beautiful work, we are all so proud of you Bryan and Tony! 

April 9, 2020

Tony Ngo's paper about a complete CXC receptor-chemokine complex and the basis of chemokine subfamily selectivity is published in PLOS Biology This is the result of a long-standing collaboration with the Handel lab. Congrats Tony, Bryan, and all!

April 2, 2020

Kirti Chahal has been awarded the CCMI training fellowship studying the oncogenic Hedgehog signaling pathway. Way to go Kirti!

September 20, 2019

The long-awaited paper by Kirti Chahal, on an unexpected activity of the approved drug Nilotinib against SMO and the Hh pathway, is now published online in  PLoS ONE. Congratulations Kirti, nice work!

July 30, 2019

Our paper on GPCR-independent activation of heterotrimeric Gi proteins  is published in PNAS! Congratulations to Nick Kalogriopoulos (Ghosh lab), Steve Reese (Chang lab), and Tony Ngo (Kufareva lab), who were in charge of biochemistry, structure determination, and computational analyses, respectively. Go team!

June 5, 2019

Please welcome Alexis Lona, the new summer intern from the Mater Dei Catholic High School. Alexis will stay with us till mid-August developing ways of analyzing the quantitative mass-spectrometry data on G protein coupled receptors, using custom code that he is writing in Python.

May 28, 2019

Weijun's new baby Anthony is here! Congratulations Weijun and family, and wishing you all lots of fun!

May 20, 2019

Margaret Misyutina, a rising second year Comp Sci major from UC Berkeley, joins our lab for the summer to try her programming skills in application to biological networks. Welcome Margaret!

April 24, 2019

Watch Adrian's stellar AP Capstone presentation about the research that he has done in our lab during the summer of 2018 and in 2019.

March 19, 2019

Congratulations to Adrian who just got accepted to MIT!

March 1, 2019

Kirti Chahal has been awarded the CCMI training fellowship for studying the oncogenic Hedgehog signaling pathway. Congratulations!

Jan 22, 2019

Kirti has been selected to participate in the ASPET Mentoring Network: Coaching for Career Development program for 2019-2020, and to receive a Mentoring Network travel award. Great work, way to go Kirti!

Nov 1, 2018

Tony's work was selected for a short talk presentation at the BPS-MPGPCR meeting in Melbourne, and awarded a travel scholarship. Congrats Tony!

Oct 8, 2018

Weijun Xu joined the group. He will be developing a novel network-based representation of GPCR signaling. Welcome Weijun!

July 2, 2018

Suchismita (Suchi) Roy joined the group as a postdoc. Welcome! Suchi will focus on biophysical studies of G protein interactions with non-receptor modulators like GIV.

January 1, 2018

Tony Ngo was awarded an NHMRC CJ Martin Early Career Fellowship. Congratulations, Tony!

June 20, 2017

Our (Immunity, 2017) publication on the structure of CCR5 with a chemokine was featured in the UC San Diego Health Sciences News (Crystallizing HIV’s Entry Point)

January 18, 2017

Our (Nature Communications, 2017) publication on the atypical chemokine receptor ACKR3 was featured in Case Western Reserve University news release “Structure of atypical cancer protein paves approach for drug development” (Jan 18, 2017, Marc Kaplan). 

See also: Health Medicine Innovation, New Medical, EurekAlert, Medical Express, and others.

May 15, 2017

Tony Ngo joined the group as a postdoc. Welcome!

February 2, 2017

Our (Nature Chemical biology, 2017) publication about GPCR COIN-Pocket and orphan receptor ligand discovery was featured in:

December 7, 2016

Our (Nature, 2016) publication on the structure of double-antagonist-bound CCR2 was reviewed in Nature News & Views article “Pharmacology: Inside-out receptor inhibition” (Dec 7, 2016, Thomas P. Sakmar and Thomas Huber), as well as the UC San Diego HS Newsroom article “Researchers Reveal 3D Structure of Cell’s Inflammation Sensor and its Inhibitors” (December 07, 2016, Heather Buschman, PhD). 

See also: Genetic Engineering and Biotechnology News, Science Newsline, Phys.org, Science Daily

January 2016

According to 2015 Journal Citation Reports® Science Edition (Thomson Reuters, 2016), our (Immunology & Cell Biology, 2015) review on chemokine and chemokine receptor structure and interactions was the most cited article in 2016

March 6, 2015 

Our CXCR4:vMIP-II structure publication (Science, 2015) was featured in:

Science Perspective article “Viral chemokine mimicry” (Jörg Standfuss, Science 2015, 347 (6226), pp. 1071-1072)

The UC San Diego HS Newsroom article “Pictured Together for the First Time: a Chemokine and its Receptor” January 22, 2015, Heather Buschman, Ph.D.).

See also: Science Daily

December 23, 2014

Our PNAS publication on stoichiometry and geometry of CXCR4:CXCL12 interaction (PNAS 2014) was featured as a Research Highlight in Dec 2014 issue of Biopolymers

January 2012

Our Pocketome article (Nucleic Acids Research, 2012) has been highlighted as a featured article of the issue.