PhD/MSc Students

Iván Martín Hernández

Former members

Ignacio Garzón
Santiago García Sánchez
Pieter Chys
Erney Ramírez Aportela
Pablo Solar Rodríguez

Pablo Chacón


Birth date: 9-9-1969
Nationality: Spanish.
Marital status: Married, Two children.


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Download Dr. Chacon's Curriculum Vitae


Pablo Chacón is a biochemist and computational biologist at the Institute of Physical Chemistry (IQFR-CSIC) in Madrid, Spain, where he is the head of research of the Structural Bioinformatics Group.

ES: Pablo Chacón es un bioquímico experto en biología computacional del Instituto de Química Física (IQFR-CSIC) de Madrid donde lidera el grupo de Bioinformática Estructural

FR: Pablo Chacón est biochimiste expert en biologie computationnelle à l'Institut de chimie physique (IQFR-CSIC) de Madrid où il est responsable du groupe de Bioinformatique Structurale


I am particularly attracted to the analysis and modeling of macromolecular machines whose actions and interactions are essential for cellular function. My research interests include new hybrid methods to combine multiresolution structural information of complementary biophysical techniques (X-ray, EM, SAXS, etc.), new methods to analyze and predict the dynamical behavior of these complex systems using coarse-grained simulations (e.g Normal Mode Analysis) and, protein and nucleic acids structure modeling. More recently, I am also interested in computer-based methodologies to aid the structure rational design of new active compounds. These research lines are well supported by a wide number of collaborations.


BSc in Chemistry (1992), University Complutense of Madrid (UCM). Spain.
MSc in Biophysics (1992), UCM.
PhD in Chemistry (1999), UCM.

Research Positions held

1992-1993 Ph.D. Student in the Biophysics Group at UCM.

As a graduate student, I received rigorous training in theoretical biophysics and structural biology. Starting from a solid training in mathematics, informatics, and biophysics, I worked on prebiotic evolution models and neural networks research fields. The latter founded my BSc work.    

1994-1998 Ph.D. Student at the Centro de Investigaciones Biológicas (CIB) of the Spanish Research Council (CSIC).

My PhD work focused on shape and size determination of proteins in solution from its Small Angle X-ray Scattering profile (SAXS) using genetic algorithms. This pioneering development makes it possible to retrieve significantly more structural information from the scattering patterns than previously believed. My thesis advisors were professors J.M. Andreu CIB (CSIC) and F. Moran (UCM). During this period of time I also learned to effectively interact with experimentalists

2000-2003 Associate Researcher at The Scripps Research Institute. CA, USA.

My postdoctoral tenure at TSRI at W. Wriggers’ lab provided me the opportunity to broaden my technical experience in multi-resolution structure analysis towards the modeling of the large-scale macromolecular assemblies on the basis of low-resolution density data from electron microscopy.

2004-2007 Tenure track researcher position at CIB-CSIC.

I came back to Spain with the Ramón and Cajal tenure track program to establish my own research group to broadly work on the development and application of computational methodologies for structural biology. During this period, I secured several grants as principal investigator.

2007-2010 Research Staff Scientist at CIB-CSIC. Group Leader.

2010-present Research Staff Scientist at Institute of Physical Chemistry (IQFR-CSIC). Group Leader.

I currently have a small group of three people including myself. Our multidisciplinary team is trying to ask and answer relevant questions in structure modeling, structure flexibility, protein interactions, and drug discovery.


He is the author or co-author of more than 70 scientific papers published in peer-reviewed journals. His H-index is 35 according to Google Scholar (2020) with more than 6000 citations (the complete profile is available at The most relevant articles are:

  • JR López-Blanco, P Chacón (2019). KORP: Knowledge-based 6D potential for fast protein and loop modeling Bioinformatics 35 (17), 3013-3019
  • JL Tenthorey, et al. The structural basis of flagellin detection by NAIP5: (2017). A strategy to limit pathogen immune evasion Science 358 (6365), 888-893
  • RK Louder, Y He, JR López-Blanco, J Fang, P Chacón, E Nogales (2016) Structure of promoter-bound TFIID and model of human pre-initiation complex assembly Nature 531, 604–609
  • EH Kellogg, S Howes, SC Ti, E Ramírez-Aportela, TM Kapoor, P Chacón, E Nogales (2016) Near-atomic cryo-EM structure of PRC1 bound to the microtubule. PNAS 113 (34), 9430-9439           
  • E Ramírez-Aportela, JR López-Blanco, P Chacon   (2016) FRODOCK 2.0: Fast Protein-Protein docking server Bioinformatics 32 (15), 2386-8       
  • JR Lopez-Blanco, AJ Canosa-Valls, Y Li, P Chacon (2016) RCD+: Fast loop modeling server  Nucleic Acids Research 44 (W1), W395-400
  • M Artola, LB Ruiz-Avila, A Vergoñós, S Huecas, L Araujo-Bazán et al. (2015)Effective GTP-replacing FtsZ Inhibitors and Antibacterial Mechanism of Action ACS chemical biology 10 (3), 834-43
  • López-Blanco J.R., Aliaga J., Quintana-Ortí E. and Chacón P. (2014) iMODS: Internal Coordinates Normal Mode Analysis Server. Nucleic acids research. 42:W271-6
  • Ramírez-Aportela E., López-Blanco J.R., Andreu J.M., and Chacón P. (2014). Understanding Nucleotide-Regulated FtsZ Filament Dynamics and the Monomer Assembly Switch with Large-Scale Atomistic Simulations. Biophys J. 107 (9):2164–2176.
  • López-Blanco J.R. and Chacón P. (2013). iMODFIT: efficient and robust flexible fitting based on vibrational analysis in internal coordinates. JSB 184(2):261–270
  • Estrin E., J.R. López-Blanco, P. Chacón, A. Martin. (2013). Formation of an intricate helical bundle dictates the assembly of the 26S proteasome lid. Structure, 21: 1624–35
  • Lopéz-Blanco J.R., J.I. Garzón and P. Chacón (2011) iMod: multipurpose normal mode analysis in internal coordinates. Bioinformatics 27 (20): 2843-2850.
  • Garzon J.I., J.R. López-Blanco, C. Pons, J. Kovacs, R. Abagyan, J. Fernandez-Recio, P. Chacón (2009) FRODOCK: a new approach for fast rotational protein-protein docking Bioinformatics, 25, 2544-2551.
  • Garzón J.I., J. Kovacs, R. Abagyan, and P. Chacón. (2007) ADP_EM: Fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics. 23(4):427-3.
  • Rueda M., P. Chacón, and M. Orozco (2007). Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics. Structure. 15(5),  565-575.
  • Opalka N., M. Chlenov, P. Chacón, W. J. Rice, W. Wriggers, and S.A. Darst (2003). Structure and Function of the Transcription Elongation Factor GreB Bound to Bacterial RNA Polymerase. Cell, 114: 335-345.
  • Chacón P. and W. Wriggers (2003). Multi-Resolution Contour-Based Fitting of Macromolecular Structures. J. Mol. Biol., 317:375-384.
  • Chacón P., Morán F, Díaz JF, and Andreu JM. (2000)  Shape and size determination from protein x-ray solution scattering with a genetic algorithm. J.Mol.Biol., 299:1289-1302.
  • Chacón P., F. Morán, J. F. Díaz, E. Pantos, and J. M. Andreu (1998).  Low-Resolution Structures of Proteins in Solution Retrieved from X-Ray Scattering with a Genetic Algorithm, Biophys. J., 74: 2760-2775.
  • Andrade, M.A., P. Chacón, J.J. Merelo and F. Morán. (1993). Evaluation of secondary structure of proteins from UV circular dichroism using an unsupervised learning neural network. Prot. Eng. 6, 383-390.

For a complete list of publications see


I regularly collaborate in different Ph.D. programs giving seminars and courses. I was advisor of four PhD theses:

  • J.I. Garzón. (2010) in Computer Engineering at Complutense University Madrid (UCM).
  • José Ramón Lopéz-Blanco (2012) in Chemistry at Complutense University of Madrid (UCM)
  • Santiago García Sánchez (2015) in Computer Engineering at Universidad Juan Carlos I (URJC)
  • Erney Ramirez-Aportela (2016) in Biophysics at Autonoma University of Madrid (UAM) 


2004-2005 Fundación BBVA (PI) .
2004-2006 MEC BFU2004-01282/BMC (PI).
2007-2009 MEC-BFU2007-65977/BMC (PI).
2007-2010 CAM-SBIO-0214-2006 (co-PI).
2008-2012 Human Frontier Science Program - RGP0039/2008 (co-PI).
2009-2012 MINECO-BFU2009-09552/BMC (PI).
2012-2016 CAM-S2010/BMD-2353 (co-PI).
2013-2016 MINECO BFU2013-44306-P(PI) .
2017-2020 MINECO-BFU2016-76220-P (PI).
2020-2023 MECD-PID2019-109041GB-C21


1995-1999 Spanish predoctoral fellowship Ref: FP94-35310411 (B.0.E. 23.11.94).
2000-2001-2003 Postdoctoral training award from the La Jolla Interfaces in Science Interdisciplinary Training Program/Burroughs Wellcome Fund.
2001-2003 Spanish Post-doctoral fellowship Ref. EX2001-35310411 (B.0.E. 2.11.2000).
2004-2007 Tenure Track Scientist Ramón y Cajal.


Biophysical Society, Spanish Biophysical Society, Sociedad Española de Bioquímica y Biología Molecular (SEBBM).