Hi, I'm a researcher in molecular biophysics at University of California, San Francisco. Please visit my research page.

About Me

Who is Ignacia Echeverria

I am currently an Assistant Professor at UCSF working on computational structural biology and molecular biophysics. Previously I was a postdoctoral researcher UCSF at Prof. Andrej Šali laboratory and at University of Maryland at Prof. Garyk Papoian. I obtained a Ph.D. in Molecular Biophysics at Johns Hopkins University and a bachelors degree in Physics at Pontificia Universidad Católica de Chile.

My research is focused on building integrative, computational, and theoretical models to describe the structure and dynamics of proteins, nucleic acids, and carbohydrates to understand their function and evolution.

On my research I use theoretical and computational methods from molecular biophysics, statistical mechanics, stochastic modeling, molecular modeling, and scientific and statistical computing to understand how molecules work.

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Ignacia Echeverria, PhD
Assistant professor

Ignacia obtained her PhD at Johns Hopkins University. At UCSF her research has focused on building integrative structure models of protein assemblies.

Neelesh Soni, PhD
Postdoctoral fellow

Neelesh obtained his PhD in Computational Biology from IISER Pune. His work includes building models of the NPC basket and its interacting proteins.

Kenneth Huang, PhD
Postdoctoral fellow

Kenneth received his PhD from Georgia State University. Kenneth will work developing multi-state models of viral proteins as potential anti-viral targets.

Swathi Badrinarayanan
Student Intern

Swathi is a senior at Saint Francis High School. Her project involves building a fragment representation of viral protein to uncover if different pathogen proteins that interact with a common human protein use the same binding motifs.


Li, Yen-Li, Caroline A. Langley, Caleigh M. Azumaya, Ignacia Echeverria, Nicholas M. Chesarino, Michael Emerman, Yifan Cheng, and John D. Gross. "The structural basis for HIV-1 Vif antagonism of human APOBEC3G." Nature (2023): 1-3. [LINK]

Kim, Sun Kyung, Miles Sasha Dickinson, Janet Finer-Moore, Ziqiang Guan, Robyn M. Kaake, Ignacia Echeverria, Jen Chen et al. "Structure and dynamics of the essential endogenous mycobacterial polyketide synthase Pks13." Nature Structural & Molecular Biology (2023): 1-13. [LINK]

Bouhaddou, Mehdi, Ann-Kathrin Reuschl, Benjamin J. Polacco, Lucy G. Thorne, Manisha R. Ummadi, Chengjin Ye, Romel Rosales et al. "SARS-CoV-2 Variants Evolve Convergent Strategies to Remodel the Host Response (preprint)." (2023). [LINK]

Echeverria, Ignacia, Hannes Braberg, Andrej Sali, and Nevan J. Krogan. Integrative structure determination of histones H3 and H4 using genetic interactions. FEBS J, (2022). [LINK] <

Braberg, Hannes, Ignacia Echeverria, Robyn M. Kaake, Andrej Sali, and Nevan J. Krogan. "From systems to structure—using genetic data to model protein structures." Nature Reviews Genetics (2022): 1-13.[LINK]

Akey, Christopher W.*, Digvijay Singh*, Christna Ouch*, Ignacia Echeverria*, Ilona Nudelman, Joseph M. Varberg, Zulin Yu et al. "Comprehensive structure and functional adaptations of the yeast nuclear pore complex." Cell (2022).[LINK]

Huang, Fang, Trang TT Nguyen, Ignacia Echeverria, Ramachandran Rakesh, Daniele C. Cary, Hana Paculova, Andrej Sali, Arthur Weiss, Boris Matija Peterlin, and Koh Fujinaga. "Reversible phosphorylation of cyclin T1 promotes assembly and stability of P-TEFb." Elife 10 (2021): e68473.

Kaake, Robyn M.*, Ignacia Echeverria*, Seung Joong Kim, John Von Dollen, Nicholas M. Chesarino, Yuqing Feng, Clinton Yu et al. "Characterization of an A3G-VifHIV-1-CRL5-CBFβ Structure Using a Cross-linking Mass Spectrometry Pipeline for Integrative Modeling of Host–Pathogen Complexes." Molecular & Cellular Proteomics 20 (2021).

Saltzberg, Daniel J., Shruthi Viswanath, Ignacia Echeverria, Ilan E. Chemmama, Ben Webb, and Andrej Sali. "Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure." Protein Science 30, no. 1 (2021): 250-261.

Braberg, Hannes*, Ignacia Echeverria*, Stefan Bohn, Peter Cimermancic, Anthony Shiver, Richard Alexander, Jiewei Xu et al. "Genetic interaction mapping informs integrative structure determination of protein complexes." Science 370, no. 6522 (2020).

Kwon, Yonghwa, Robyn Kaake, Ignacia Echeverria, Marissa Suarez, Charlotte Stoneham, Peter W. Ramirez, Jacob Kress et al. "Structural Basis of CD4 Downregulation by HIV-1 Nef." bioRxiv (2020). [PDF]

Gutierrez, Craig, Ilan E. Chemmama, Haibin Mao, Clinton Yu, Ignacia Echeverria, Sarah A. Block, Scott D. Rychnovsky, Ning Zheng, Andrej Sali, and Lan Huang. "Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling." Proceedings of the National Academy of Sciences 117, no. 8 (2020): 4088-4098. [PDF]

Saltzberg, Daniel, Charles H. Greenberg, Shruthi Viswanath, Ilan Chemmama, Ben Webb, Riccardo Pellarin, Ignacia Echeverria, and Andrej Sali. "Modeling biological complexes using integrative modeling platform." In Biomolecular Simulations, pp. 353-377. Humana, New York, NY, 2019.

Kim, Seung Joong, Javier Fernandez-Martinez, Ilona Nudelman, Yi Shi, Wenzhu Zhang, Barak Raveh, Thurston Herricks, J.A. Hogan, Paula Upla. Ilan Chemmama, Riccardo Pellarin, Ignacia Echeverria, et al. "Integrative structure and functional anatomy of a nuclear pore complex." Microscopy and Microanalysis 24, no. S1 (2018): 1212-1213. [PDF]

Kim, Seung Joong, Javier Fernandez-Martinez, Ilona Nudelman, Yi Shi, Wenzhu Zhang, Barak Raveh, Thurston Herricks, J.A. Hogan, Paula Upla. Ilan Chemmama, Riccardo Pellarin, Ignacia Echeverria, et al. "Integrative structure and functional anatomy of a nuclear pore complex." Nature 555, no. 7697 (2018): 475. [PDF]

Zhuo, Coral Y.; Caitlin I. Stoddard; Jonathan B. Johnston; Michael J. Trnka; Ignacia Echeverria; Eugene Palovcak; Andrej Sali; Alma L. Burlingame; Yifan Cheng; Geeta J. Narlikar "Correspondence information about the; Geeta J. Narlikar "Regulation of Rvb1/Rvb2 by a Domain within the INO80 Chromatin Remodeling Complex Implicates the Yeast Rvbs as Protein Assembly Chaperones" Cell Reports (2017). [PDF]

Schulze-Gahmen, Ursula; Ignacia Echeverria,; Goran Stjepanovic; Yun Bai; Huasong Lu; Dina Schneidman-Duhovny; Jennifer Doudna; Qiang Zhou; Andrej Sali; James Hurley "Insights into HIV-1 proviral transcription from an integrative structure of the P- TEFb:AFF4:Tat:TAR complex" eLife Journal (2016). [PDF]

Ferrandino, Giuseppe; Juan Pablo Nicola; Yuly E. Sánchez; Echeverria, Ignacia; Yunlong Liu; L Mario Amzel; Nancy Carrasco "Na+ coordination at the Na2 site of the Na+/I− symporter" PNAS (2016). [PDF]

Echeverria, Ignacia; Yunlong Liu; Sandra B Gabelli; L Mario Amzel "PI3Kα oncogenic mutations weaken the interactions that stabilize the p110α/p85α heterodimer" FEBS Journal (2015). [PDF]

Winogradoff, David*; Echeverria, Ignacia*; Davit A Potoyan, and Garegin A. Papoian. "The acetylation landscape of the H4 histone tail: disentangling the interplay between the specific and cumulative effects." Journal of the American Chemical Society (2015). [PDF]

Echeverria, Ignacia and Garegin A. Papoian. "DNA Exit Ramps Are Revealed in the Binding Landscapes Obtained from Simulations in Helical Coordinates." PLoS Comput Biol 11(2): (2015). [LINK]

Echeverria, Ignacia and Garegin A. Papoian. "Perspectives on the coarse-graining models of DNA molecules" in Many-body effects and electrostatics in multi-scale computations of Biomolecules, Eds. Qiang Cui, Pengyu Ren and Markus Meuwly (Book chapter) [LINK]

Echeverria, Ignacia and Garegin A. Papoian. "Structural heterogeneity and dynamics of the unfolded ensemble" Isr. J. Chem. 53 (2014). [PDF]

Echeverria, Ignacia; Dmitrii E. Makarov; and Garegin A. Papoian. "Concerted dihedral rotations give rise to internal friction in unfolded proteins." Journal of the American Chemical Society 136,(2014): 8708–8713. [PDF] Highlighted in JACS select [LINK]

Echeverria, Ignacia, and L. Mario Amzel. "Estimation of Free-Energy Differences from Computed Work Distributions: An Application of Jarzynski’s Equality." The Journal of Physical Chemistry B 116.36 (2012): 10986-10995. [PDF]

Gabelli, Sandra B.; Echeverria, Ignacia et al. "Activation of PI3Kα by physiological effectors and by oncogenic mutations: structural and dynamic effects." Biophysical Reviews: 1-7. [LINK]

Echeverria, Ignacia, and L. Mario Amzel. "Disaccharide binding to galectin-1: free energy calculations and molecular recognition mechanism." Biophysical journal 100.9 (2011): 2283-2292. [PDF]

Echeverria, Ignacia, and L. Mario Amzel. "Helix propensities calculations for amino acids in alanine based peptides using Jarzynski's equality." Proteins: Structure, Function, and Bioinformatics 78.5 (2010): 1302-1310. [PDF]

Messing, Simon AJ, et al. "Structural insights into maize viviparous14, a key enzyme in the biosynthesis of the phytohormone abscisic acid." The Plant Cell 22.9 (2010): 2970-2980. [LINK]

Urquiza, Mauricio, et al. "α-Helix peptides designed from EBV-gH protein display higher antigenicity and induction of monocyte apoptosis than the native peptide." Amino acids 39.5 (2010): 1507-1519. [LINK]


The QCRG AVIDD Program

"The QCRG (Quantitative Biosciences Institute Coronavirus Research Group) AViDD Program is an interdisciplinary program that aims to identify new direct-acting antivirals for SARS-CoV-2 and 19 other viruses."


The HIV Accessory and Regulatory Complexes (HARC) center

"HARC is a collaborative research center to study HIV Accessory and Regulatory Complexes."


The National Center for Dynamic Interactome Research (NCDIR)

"The NCDIR center goal is develop technologies to reveal, analyze and interpret interactomes in numerous biological and hierarchical cellular contexts. "


IMP, the Integrative Modeling Platform

"IMP is an open-source, comprehensive, and extensible software that provides programmatic support for developing and distributing integrative structure modeling protocols"




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