Pepe, A., Lasenby, J., & Chacon, P. (2024). Geometric Algebra Models of Proteins for Three-Dimensional Structure Prediction: A Detailed Analysis. Advanced Computational Applications of Geometric Algebra, 141–159. https://doi.org/10.1007/978-3-031-55985-3_6

Alcorlo, M., Luque-Ortega, J. R., Gago, F., Ortega, A., Castellanos, M., Chacón, P., de Vega, M., Blanco, L., Hermoso, J. M., Serrano, M., Rivas, G., & Hermoso, J. A. (2024). Flexible structural arrangement and DNA-binding properties of protein p6 from Bacillus subtillis phage φ29. Nucleic Acids Research, 52(4), 2045–2065. https://doi.org/10.1093/nar/gkae041

Pepe, A., Lasenby, J., & Chacón, P. (2023). Using a Graph Transformer Network to Predict 3D Coordinates of Proteins via Geometric Algebra Modelling. Empowering Novel Geometric Algebra for Graphics and Engineering, 83–95. https://doi.org/10.1007/978-3-031-30923-6_7

Hernández, I. M., Dehouck, Y., Bastolla, U., López-Blanco, J. R., & Chacón, P. (2023). Predicting protein stability changes upon mutation using a simple orientational potential. Bioinformatics, 39(1). https://doi.org/10.1093/bioinformatics/btad011

Gao, Z., Tan, C., Chacón, P., & Li, S. Z. (2022). PiFold: Toward effective and efficient protein inverse folding (Version 4). arXiv. https://doi.org/10.48550/ARXIV.2209.12643

Bueno-Carrasco, M. T., Cuéllar, J., Flydal, M. I., Santiago, C., Kråkenes, T.-A., Kleppe, R., López-Blanco, J. R., Marcilla, M., Teigen, K., Alvira, S., Chacón, P., Martinez, A., & Valpuesta, J. M. (2022). Structural mechanism for tyrosine hydroxylase inhibition by dopamine and reactivation by Ser40 phosphorylation. Nature Communications, 13(1). https://doi.org/10.1038/s41467-021-27657-y

Pepe, A., Lasenby, J., & Chacón, P. (2022). Learning rotations. Mathematical Methods in the Applied Sciences, 47(3), 1204–1217. Portico. https://doi.org/10.1002/mma.8698

López-Blanco, J. R., Dehouck, Y., Bastolla, U., & Chacón, P. (2022). Local Normal Mode Analysis for Fast Loop Conformational Sampling. Journal of Chemical Information and Modeling, 62(18), 4561–4568. https://doi.org/10.1021/acs.jcim.2c00870

Barozet, A., Chacón, P., & Cortés, J. (2021). Current approaches to flexible loop modeling. Current Research in Structural Biology, 3, 187–191. https://doi.org/10.1016/j.crstbi.2021.07.002

Quignot, C., Postic, G., Bret, H., Rey, J., Granger, P., Murail, S., Chacón, P., Andreani, J., Tufféry, P., & Guerois, R. (2021). InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps. Nucleic Acids Research, 49(W1), W277–W284. https://doi.org/10.1093/nar/gkab358

Valpuesta, J., Bueno-Carrasco, T., Cuellar, J., Flydal, M., Santiago, C., Kråkenes, T.-A., Kleppe, R., López-Blanco, J., Teigen, K., Alvira, S., Chacon, P., & Martínez, A. (2020). The Structure of Human Tyrosine Hydroxylase Reveals the Mechanism for Feedback Inhibition by Dopamine. https://doi.org/10.21203/rs.3.rs-64971/v1

Melero, R., Sorzano, C. O. S., Foster, B., Vilas, J.-L., Martínez, M., Marabini, R., Ramírez-Aportela, E., Sanchez-Garcia, R., Herreros, D., del Caño, L., Losana, P., Fonseca-Reyna, Y. C., Conesa, P., Wrapp, D., Chacon, P., McLellan, J. S., Tagare, H. D., & Carazo, J.-M. (2020). Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures. https://doi.org/10.1101/2020.07.08.191072

Quignot, C., Granger, P., Chacón, P., Guerois, R., & Andreani, J. (2020). Atomic-level evolutionary information improves protein-protein interface scoring. https://doi.org/10.1101/2020.10.26.355073

Kadukova, M., Machado, K. dos S., Chacón, P., & Grudinin, S. (2020). KORP-PL: a coarse-grained knowledge-based scoring function for protein–ligand interactions. Bioinformatics, 37(7), 943–950. https://doi.org/10.1093/bioinformatics/btaa748

López-Blanco, J. R., & Chacón, P. (2019). KORP: knowledge-based 6D potential for fast protein and loop modeling. Bioinformatics, 35(17), 3013–3019. https://doi.org/10.1093/bioinformatics/btz026

Artola, M., Ruíz-Avila, L. B., Ramírez-Aportela, E., Martínez, R. F., Araujo-Bazán, L., Vázquez-Villa, H., Martín-Fontecha, M., Oliva, M. A., Martín-Galiano, A. J., Chacón, P., López-Rodríguez, M. L., Andreu, J. M., & Huecas, S. (2017). The structural assembly switch of cell division protein FtsZ probed with fluorescent allosteric inhibitors. Chemical Science, 8(2), 1525–1534. https://doi.org/10.1039/c6sc03792e

Tenthorey, J. L., Haloupek, N., López-Blanco, J. R., Grob, P., Adamson, E., Hartenian, E., Lind, N. A., Bourgeois, N. M., Chacón, P., Nogales, E., & Vance, R. E. (2017). The structural basis of flagellin detection by NAIP5: A strategy to limit pathogen immune evasion. Science, 358(6365), 888–893. https://doi.org/10.1126/science.aao1140

Louder, R. K., He, Y., López-Blanco, J. R., Fang, J., Chacón, P., & Nogales, E. (2016). Structure of promoter-bound TFIID and model of human pre-initiation complex assembly. Nature, 531(7596), 604–609. https://doi.org/10.1038/nature17394

López-Blanco, J. R., Canosa-Valls, A. J., Li, Y., & Chacón, P. (2016). RCD+: Fast loop modeling server. Nucleic Acids Research, 44(W1), W395–W400. https://doi.org/10.1093/nar/gkw395

López-Blanco, J. R., & Chacón, P. (2016). New generation of elastic network models. Current Opinion in Structural Biology, 37, 46–53. https://doi.org/10.1016/j.sbi.2015.11.013

Kellogg, E. H., Howes, S., Ti, S.-C., Ramírez-Aportela, E., Kapoor, T. M., Chacón, P., & Nogales, E. (2016). Near-atomic cryo-EM structure of PRC1 bound to the microtubule. Proceedings of the National Academy of Sciences, 113(34), 9430–9439. https://doi.org/10.1073/pnas.1609903113

Ramírez-Aportela, E., López-Blanco, J. R., & Chacón, P. (2016). FRODOCK 2.0: fast protein–protein docking server. Bioinformatics, 32(15), 2386–2388. https://doi.org/10.1093/bioinformatics/btw141

Aliaga, J. I., Alonso, P., Badía, J. M., Chacón, P., Davidović, D., López-Blanco, J. R., & Quintana-Ortí, E. S. (2016). A fast band–Krylov eigensolver for macromolecular functional motion simulation on multicore architectures and graphics processors. Journal of Computational Physics, 309, 314–323. https://doi.org/10.1016/j.jcp.2016.01.007

Ramírez-Aportela, E., López-Blanco, J. R., Andreu, J. M., & Chacon, P. (2015). Molecular Dynamics and Assembly Switch of FtsZ Filaments. Biophysical Journal, 108(2), 527a. https://doi.org/10.1016/j.bpj.2014.11.2889

Canosa-Valls, A. J., Ramírez-Aportela, E., Chacón, P., & López-Blanco, J. R. (2015). Integrative Modeling Approaches to Interpret High-Resolution cryo-EM Reconstructions. Biophysical Journal, 108(2), 472a. https://doi.org/10.1016/j.bpj.2014.11.2582

Ramírez-Aportela, E., López-Blanco, J. R., Andreu, J. M., & Chacón, P. (2014). Understanding Nucleotide-Regulated FtsZ Filament Dynamics and the Monomer Assembly Switch with Large-Scale Atomistic Simulations. Biophysical Journal, 107(9), 2164–2176. https://doi.org/10.1016/j.bpj.2014.09.033

Silva-Martín, N., Bartual, S. G., Ramírez-Aportela, E., Chacón, P., Park, C. G., & Hermoso, J. A. (2014). Structural Basis for Selective Recognition of Endogenous and Microbial Polysaccharides by Macrophage Receptor SIGN-R1. Structure, 22(11), 1595–1606. https://doi.org/10.1016/j.str.2014.09.001

López‐Blanco, J. R., Miyashita, O., Tama, F., & Chacón, P. (2014). Normal Mode Analysis Techniques in Structural Biology. Encyclopedia of Life Sciences. Portico. https://doi.org/10.1002/9780470015902.a0020204.pub2

López-Blanco, J. R., Ramirez, E., Garcia, S., & Chacon, P. (2014). Imods: Fast Exploration of Macromolecular Collective Motions. Biophysical Journal, 106(2), 653a. https://doi.org/10.1016/j.bpj.2013.11.3614

López-Blanco, J. R., Aliaga, J. I., Quintana-Ortí, E. S., & Chacón, P. (2014). iMODS: internal coordinates normal mode analysis server. Nucleic Acids Research, 42(W1), W271–W276. https://doi.org/10.1093/nar/gku339

Sanchez, S. G., Aportela, E. R., Garzon, J. I., Chacon, P., Montemayor, A. S., & Cabido, R. (2014). FRODRUG: A Virtual Screening GPU Accelerated Approach for Drug Discovery. 2014 22nd Euromicro International Conference on Parallel, Distributed, and Network-Based Processing, 594–600. https://doi.org/10.1109/pdp.2014.64

Krüger, D. M., Ignacio Garzón, J., Chacón, P., & Gohlke, H. (2014). DrugScorePPI Knowledge-Based Potentials Used as Scoring and Objective Function in Protein-Protein Docking. PLoS ONE, 9(2), e89466. https://doi.org/10.1371/journal.pone.0089466

López‐Blanco, J. R., & Chacón, P. (2014). Structural modeling from electron microscopy data. WIREs Computational Molecular Science, 5(1), 62–81. Portico. https://doi.org/10.1002/wcms.1199

Artola, M., Ruiz-Avila, L. B., Vergoñós, A., Huecas, S., Araujo-Bazán, L., Martín-Fontecha, M., Vázquez-Villa, H., Turrado, C., Ramírez-Aportela, E., Hoegl, A., Nodwell, M., Barasoain, I., Chacón, P., Sieber, S. A., Andreu, J. M., & López-Rodríguez, M. L. (2014). Effective GTP-Replacing FtsZ Inhibitors and Antibacterial Mechanism of Action. ACS Chemical Biology, 10(3), 834–843. https://doi.org/10.1021/cb500974d

Ruiz-Avila, L. B., Huecas, S., Artola, M., Vergoñós, A., Ramírez-Aportela, E., Cercenado, E., Barasoain, I., Vázquez-Villa, H., Martín-Fontecha, M., Chacón, P., López-Rodrı́guez, M. L., & Andreu, J. M. (2013). Synthetic Inhibitors of Bacterial Cell Division Targeting the GTP-Binding Site of FtsZ. ACS Chemical Biology, 8(9), 2072–2083. https://doi.org/10.1021/cb400208z

Chys, P., & Chacón, P. (2013). Random Coordinate Descent with Spinor-matrices and Geometric Filters for Efficient Loop Closure. Journal of Chemical Theory and Computation, 9(3), 1821–1829. https://doi.org/10.1021/ct300977f

Lopéz-Blanco, J. R., & Chacón, P. (2013). iMODFIT: Efficient and robust flexible fitting based on vibrational analysis in internal coordinates. Journal of Structural Biology, 184(2), 261–270. https://doi.org/10.1016/j.jsb.2013.08.010

Estrin, E., Lopez-Blanco, J. R., Chacón, P., & Martin, A. (2013). Formation of an Intricate Helical Bundle Dictates the Assembly of the 26S Proteasome Lid. Structure, 21(9), 1624–1635. https://doi.org/10.1016/j.str.2013.06.023

López-Blanco, J. R., Reyes, R., Aliaga, J. I., Badia, R. M., Chacón, P., & Quintana-Ortí, E. S. (2013). Exploring large macromolecular functional motions on clusters of multicore processors. Journal of Computational Physics, 246, 275–288. https://doi.org/10.1016/j.jcp.2013.03.032

Lopez-Blanco, J. R., Ramirez, E., Garcia, S., & Chacon, P. (2013). Exploring Macromolecular Machine Motions. Biophysical Journal, 104(2), 69a. https://doi.org/10.1016/j.bpj.2012.11.418

Chys, P., & Chacón, P. (2012). Spinor product computations for protein conformations. Journal of Computational Chemistry, 33(21), 1717–1729. Portico. https://doi.org/10.1002/jcc.23002

Pesonen, J., Henriksson, K. O. E., López-Blanco, J. R., & Chacón, P. (2012). Normal mode analysis of molecular motions in curvilinear coordinates on a non-Eckart body-frame: an application to protein torsion dynamics. Journal of Mathematical Chemistry, 50(6), 1521–1549. https://doi.org/10.1007/s10910-012-9987-8

Ramon Lopez-Blanco, J., Ramirez-Aportela, E., Garcia-Sanchez, S., Chys, P., & Chacon, P. (2012). Modeling Macromolecular Flexibility with Normal Mode Analysis in Internal Coordinates. Biophysical Journal, 102(3), 394a. https://doi.org/10.1016/j.bpj.2011.11.2155

HENRIKSSON, K. O. E., PESONEN, J., & CHACON, P. (2012). CURVILINEAR DYNAMICS OF PROTEIN COMPLEXES. Journal of Theoretical and Computational Chemistry, 11(03), 675–696. https://doi.org/10.1142/s0219633612500459

Lopéz-Blanco, J. R., Garzón, J. I., & Chacón, P. (2011). iMod: multipurpose normal mode analysis in internal coordinates. Bioinformatics, 27(20), 2843–2850. https://doi.org/10.1093/bioinformatics/btr497

Schaffner-Barbero, C., Martín-Fontecha, M., Chacón, P., & Andreu, J. M. (2011). Targeting the Assembly of Bacterial Cell Division Protein FtsZ with Small Molecules. ACS Chemical Biology, 7(2), 269–277. https://doi.org/10.1021/cb2003626

Orellana, L., Rueda, M., Ferrer-Costa, C., Lopez-Blanco, J. R., Chacón, P., & Orozco, M. (2010). Approaching Elastic Network Models to Molecular Dynamics Flexibility. Journal of Chemical Theory and Computation, 6(9), 2910–2923. https://doi.org/10.1021/ct100208e

Buey, R. M., Chacón, P., Andreu, J. M., & Díaz, J. F. (2009). Protein Shape and Assembly Studied with X-Ray Solution Scattering: Fundaments and Practice. Applications of Synchrotron Light to Scattering and Diffraction in Materials and Life Sciences, 245–263. https://doi.org/10.1007/978-3-540-95968-7_12

Boer, D. R., Ruíz-Masó, J. A., López-Blanco, J. R., Blanco, A. G., Vives-Llàcer, M., Chacón, P., Usón, I., Gomis-Rüth, F. X., Espinosa, M., Llorca, O., del Solar, G., & Coll, M. (2009). Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains. The EMBO Journal, 28(11), 1666–1678. https://doi.org/10.1038/emboj.2009.125

Garzon, J. I., Lopéz-Blanco, J. R., Pons, C., Kovacs, J., Abagyan, R., Fernandez-Recio, J., & Chacon, P. (2009). FRODOCK: a new approach for fast rotational protein–protein docking. Bioinformatics, 25(19), 2544–2551. https://doi.org/10.1093/bioinformatics/btp447

Abia, D., Bastolla, U., Chacón, P., Fábrega, C., Gago, F., Morreale, A., & Tramontano, A. (2009). In memoriam. Proteins: Structure, Function, and Bioinformatics, 78(1). Portico. https://doi.org/10.1002/prot.22660

Ignacio Garzon, J., Huedo, E., Santiago Montero, R., Martin Llorente, I., & Chacon, P. (2009). End-To-End Cache System for Grid Computing: Design and Efficiency Analysis of a High-Throughput Bioinformatic Docking Application. The International Journal of High Performance Computing Applications, 24(3), 243–264. https://doi.org/10.1177/1094342009350469

Torreira, E., Jha, S., López-Blanco, J. R., Arias-Palomo, E., Chacón, P., Cañas, C., Ayora, S., Dutta, A., & Llorca, O. (2008). Architecture of the Pontin/Reptin Complex, Essential in the Assembly of Several Macromolecular Complexes. Structure, 16(10), 1511–1520. https://doi.org/10.1016/j.str.2008.08.009

Rueda, M., Chacón, P., & Orozco, M. (2007). Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics. Structure, 15(5), 565–575. https://doi.org/10.1016/j.str.2007.03.013

Buey, R. M., Monterroso, B., Menéndez, M., Diakun, G., Chacón, P., Hermoso, J. A., & Díaz, J. F. (2007). Insights into Molecular Plasticity of Choline Binding Proteins (Pneumococcal Surface Proteins) by SAXS. Journal of Molecular Biology, 365(2), 411–424. https://doi.org/10.1016/j.jmb.2006.09.091

Garzon, J. I., Huedo, E., Montero, R. S., Llorente, I. M., & Chacon, P. (2007). Grid Multi-Resolution Docking. 15th EUROMICRO International Conference on Parallel, Distributed and Network-Based Processing (PDP’07), 3–10. https://doi.org/10.1109/pdp.2007.48

Martín-Benito, J., Gómez-Reino, J., Stirling, P. C., Lundin, V. F., Gómez-Puertas, P., Boskovic, J., Chacón, P., Fernández, J. J., Berenguer, J., Leroux, M. R., & Valpuesta, J. M. (2007). Divergent Substrate-Binding Mechanisms Reveal an Evolutionary Specialization of Eukaryotic Prefoldin Compared to Its Archaeal Counterpart. Structure, 15(1), 101–110. https://doi.org/10.1016/j.str.2006.11.006

Garzón, J. I., Kovacs, J., Abagyan, R., & Chacón, P. (2007). DFprot: a webtool for predicting local chain deformability. Bioinformatics, 23(7), 901–902. https://doi.org/10.1093/bioinformatics/btm014

Garzón, J. I., Kovacs, J., Abagyan, R., & Chacón, P. (2006). ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage. Bioinformatics, 23(4), 427–433. https://doi.org/10.1093/bioinformatics/btl625

Wriggers, W., Chacón, P., A. Kovacs, J., Tama, F., & Birmanns, S. (2004). Topology representing neural networks reconcile biomolecular shape, structure, and dynamics. Neurocomputing, 56, 365–379. https://doi.org/10.1016/j.neucom.2003.09.007

Kovacs, J. A., Chacón, P., & Abagyan, R. (2004). Predictions of protein flexibility: First‐order measures. Proteins: Structure, Function, and Bioinformatics, 56(4), 661–668. Portico. https://doi.org/10.1002/prot.20151

Boskovic, J. (2003). Visualization of DNA-induced conformational changes in the DNA repair kinase DNA-PKcs. The EMBO Journal, 22(21), 5875–5882. https://doi.org/10.1093/emboj/cdg555

Opalka, N., Chlenov, M., Chacon, P., Rice, W. J., Wriggers, W., & Darst, S. A. (2003). Structure and Function of the Transcription Elongation Factor GreB Bound to Bacterial RNA Polymerase. Cell, 114(3), 335–345. https://doi.org/10.1016/s0092-8674(03)00600-7

Chacón, P., Tama, F., & Wriggers, W. (2003). Mega-Dalton Biomolecular Motion Captured from Electron Microscopy Reconstructions. Journal of Molecular Biology, 326(2), 485–492. https://doi.org/10.1016/s0022-2836(02)01426-2

Kovacs, J. A., Chacón, P., Cong, Y., Metwally, E., & Wriggers, W. (2003). Fast rotational matching of rigid bodies by fast Fourier transform acceleration of five degrees of freedom. Acta Crystallographica Section D Biological Crystallography, 59(8), 1371–1376. https://doi.org/10.1107/s0907444903011247

Chacón, P., & Wriggers, W. (2002). Multi-resolution contour-based fitting of macromolecular structures. Journal of Molecular Biology, 317(3), 375–384. https://doi.org/10.1006/jmbi.2002.5438

Darst, S. A., Opalka, N., Chacon, P., Polyakov, A., Richter, C., Zhang, G., & Wriggers, W. (2002). Conformational flexibility of bacterial RNA polymerase. Proceedings of the National Academy of Sciences, 99(7), 4296–4301. https://doi.org/10.1073/pnas.052054099

Wriggers, W., & Chacón, P. (2001). UsingSitusfor the registration of protein structures with low-resolution bead models from X-ray solution scattering. Journal of Applied Crystallography, 34(6), 773–776. https://doi.org/10.1107/s0021889801012869

Wriggers, W., & Chacón, P. (2001). Modeling Tricks and Fitting Techniques for Multiresolution Structures. Structure, 9(9), 779–788. https://doi.org/10.1016/s0969-2126(01)00648-7

Dı́az, J. F., Valpuesta, J. M., Chacón, P., Diakun, G., & Andreu, J. M. (1998). Changes in Microtubule Protofilament Number Induced by Taxol Binding to an Easily Accessible Site. Journal of Biological Chemistry, 273(50), 33803–33810. https://doi.org/10.1074/jbc.273.50.33803

Lambeir, A.-M., Dı́az Pereira, J. F., Chacón, P., Vermeulen, G., Heremans, K., Devreese, B., Van Beeumen, J., De Meester, I., & Scharpé, S. (1997). A prediction of DPP IV/CD26 domain structure from a physico-chemical investigation of dipeptidyl peptidase IV (CD26) from human seminal plasma. Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, 1340(2), 215–226. https://doi.org/10.1016/s0167-4838(97)00045-9

de Pereda, J. M., Leynadier, D., Evangelio, J. A., Chacón, P., & Andreu, J. M. (1996). Tubulin Secondary Structure Analysis, Limited Proteolysis Sites, and Homology to FtsZ. Biochemistry, 35(45), 14203–14215. https://doi.org/10.1021/bi961357b

Chacón, P., & Nuño, J. C. (1995). Spatial dynamics of a model for prebiotic evolution. Physica D: Nonlinear Phenomena, 81(4), 398–410. https://doi.org/10.1016/0167-2789(94)00214-b

Advances in Artificial Life. (1995). In F. Morán, A. Moreno, J. J. Merelo, & P. Chacón (Eds.), Lecture Notes in Computer Science. Springer Berlin Heidelberg. https://doi.org/10.1007/3-540-59496-5

Nuño, J. C., Chacón, P., Moreno, A., & Morán, F. (1995). Compartimentation in replicator models. Advances in Artificial Life, 116–127. https://doi.org/10.1007/3-540-59496-5_293

Höfer, T., Maini, P. K., Sherratt, J. A., Chaplain, M. A. J., Chauvet, P., Metevier, D., Montes, P. C., & Murray, J. D. (1994). A resolution of the chemotactic wave paradox. Applied Mathematics Letters, 7(2), 1–5. https://doi.org/10.1016/0893-9659(94)90020-5

Andrade, M. A., Chacón, P., Merelo, J. J., & Morán, F. (1993). Evaluation of secondary structure of proteins from UV circular dichroism spectra using an unsupervised learning neural network. “Protein Engineering, Design and Selection,” 6(4), 383–390. https://doi.org/10.1093/protein/6.4.383