Pablo Chacón
Biography
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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. |
Profile
| Institution | IQF |
| Position | Investigador principal |
| Home page | https://chacolab.org |
| Contact email | pchacon@iqf.csic.es |
| ORCID | 0000-0002-3168-4826 |
BCB Hub
| BCB Committee | Expertise mapping |
| BCB Tools | RCD+, IMOD, FRODOCK |
| BCB Services |
Research
Research topics
Computational MethodsData AnalysisArtificial IntelligenceStructural bioinformaticsExperimental structure determinationMolecular flexibilityComputational models and simulationsMutation Analysis and designBiomolecular simulationStructure-function relationshipStructure predictionMolecular Interactions/Docking
View all (2 more)
Deep Learning in BiologyProtein/Nucleic Acid design
Research lines
Projects, networks, transfer & teaching
Funded projects 2
Publications 93 entries
- Flexible structural arrangement and DNA-binding properties of protein p6 from Bacillus subtillis phage ϕ29 Article · 28 Jan 2024
- Geometric Algebra Models of Proteins for Three-Dimensional Structure Prediction: A Detailed Analysis Book / chapter · 2024
- Predicting protein stability changes upon mutation using a simple orientational potential Article · 1 Jan 2023
- Using a Graph Transformer Network to Predict 3D Coordinates of Proteins via Geometric Algebra Modelling Book / chapter · 2023
- Local Normal Mode Analysis for Fast Loop Conformational Sampling Article · 13 Sep 2022
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- Learning rotations Article · 11 Sep 2022
- Structural mechanism for tyrosine hydroxylase inhibition by dopamine and reactivation by Ser40 phosphorylation Article · 10 Jan 2022
- PIFOLD: TOWARD EFFECTIVE AND EFFICIENT PROTEIN INVERSE FOLDING Preprint · 2022
- 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 Article · 12 May 2021
- Atomic-level evolutionary information improves protein–protein interface scoring Article · 26 Apr 2021
- Current approaches to flexible loop modeling Article · 2021
- Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures Article · 29 Sep 2020
- The Structure of Human Tyrosine Hydroxylase Reveals the Mechanism for Feedback Inhibition by Dopamine Preprint · 16 Sep 2020
- KORP-PL: a coarse-grained knowledge-based scoring function for protein–ligand interactions Article · 25 Aug 2020
- KORP: Knowledge-based 6D potential for fast protein and loop modeling Article · 14 Jan 2019
- The structural basis of flagellin detection by NAIP5: A strategy to limit pathogen immune evasion Article · 17 Nov 2017
- The structural assembly switch of cell division protein FtsZ probed with fluorescent allosteric inhibitors Article · 2017
- Near-atomic cryo-EM structure of PRC1 bound to the microtubule Article · 4 Aug 2016
- RCD plus : Fast loop modeling server Software · 5 May 2016
- New generation of elastic network models Article · Apr 2016
- Structure of promoter-bound TFIID and model of human pre-initiation complex assembly Article · 23 Mar 2016
- FRODOCK 2.0: fast protein-protein docking server. Software · 12 Mar 2016
- A fast band-Krylov eigensolver for macromolecular functional motion simulation on multicore architectures and graphics processors Article · Mar 2016
- Molecular Dynamics and Assembly Switch of FtsZ Filaments Article · Jan 2015
- Integrative Modeling Approaches to Interpret High-Resolution cryo-EM Reconstructions Article · Jan 2015
- Effective GTP-replacing FtsZ inhibitors and antibacterial mechanism of action Article · 30 Dec 2014
- Understanding nucleotide-regulated FtsZ filament dynamics and the monomer assembly switch with large-scale atomistic simulations Article · Nov 2014
- Structural basis for selective recognition of endogenous and microbial polysaccharides by macrophage receptor SIGN-R1 Article · Nov 2014
- Normal mode analysis in structural biology Other · 15 Oct 2014
- Structural modeling from electron microscopy data Article · 15 Sep 2014
- IMODS: Internal coordinates normal mode analysis server Software · 25 Apr 2014
- DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking Article · 21 Feb 2014
- FRODRUG: A virtual screening GPU accelerated approach for drug discovery Conference paper · Feb 2014
- Imods: Fast Exploration of Macromolecular Collective Motions Article · Jan 2014
- Targeting bacterial cell division protein FtsZ with small molecules and fluorescent probes Article · 2014
- IMODFIT: Efficient and robust flexible fitting based on vibrational analysis in internal coordinates Article · Nov 2013
- Formation of an intricate helical bundle dictates the assembly of the 26S proteasome Lid Article · Sep 2013
- Exploring large macromolecular functional motions on clusters of multicore processors Article · Aug 2013
- Synthetic inhibitors of bacterial cell division targeting the GTP-binding site of FtsZ Article · 31 Jul 2013
- Random coordinate descent with spinor-matrices and geometric filters for efficient loop closure Article · 4 Mar 2013
- Exploring Macromolecular Machine Motions Article · Jan 2013
- Curvilinear dynamics of protein complexes Article · Jun 2012
- Spinor product computations for protein conformations Article · 8 May 2012
- Normal mode analysis of molecular motions in curvilinear coordinates on a non-Eckart body-frame: An application to protein torsion dynamics Article · 11 Mar 2012
- Modeling Macromolecular Flexibility with Normal Mode Analysis in Internal Coordinates Article · Jan 2012
- Ultra-fast registration of 2d electron microscopy images Article · 2012
- Addressing macromolecular flexibility Article · 2012
- Targeting the assembly of bacterial cell division protein FtsZ with small molecules Article · 15 Nov 2011
- iMod: Multipurpose normal mode analysis in internal coordinates Article · 27 Aug 2011
- Predicting Protein-protein Interactions with DrugScorePPI: Docking, Scoring, and in silico Alanine-scanning Article · 19 Apr 2011
- Approaching elastic network models to molecular dynamics flexibility Article · 20 Aug 2010
- In memoriam. Angel Ramírez Ortiz (1966-2008). Article · 27 Nov 2009
- End-to-end cache system for grid computing: Design and efficiency analysis of a high-throughput bioinformatic docking application Article · 2 Nov 2009
- Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains Article · 14 May 2009
- Structural features of the replication initiator protein RepB of the promiscuous plasmid pMV158 Article · 2009
- Protein shape and assembly studied with X-ray solution scattering: Fundaments and practice Book / chapter · 2009
- Architecture of the Pontin/Reptin Complex, Essential in the Assembly of Several Macromolecular Complexes Article · Oct 2008
- Adaptation of a multi-resolution docking bioinformatics application to the grid Article · 1 Aug 2007
- Thorough Validation of Protein Normal Mode Analysis: A Comparative Study with Essential Dynamics Article · May 2007
- DFprot: A webtool for predicting local chain deformability Article · 3 Feb 2007
- Grid multi-resolution docking Conference paper · Feb 2007
- Insights into Molecular Plasticity of Choline Binding Proteins (Pneumococcal Surface Proteins) by SAXS Article · Jan 2007
- Divergent Substrate-Binding Mechanisms Reveal an Evolutionary Specialization of Eukaryotic Prefoldin Compared to Its Archaeal Counterpart Article · Jan 2007
- ADP_EM: Fast exhaustive multi-resolution docking for high-throughput coverage Article · 6 Dec 2006
- Predictions of protein flexibility: First-order measures Article · 20 May 2004
- Topology representing neural networks reconcile biomolecular shape, structure, and dynamics Article · Jan 2004
- Visualization of DNA-induced conformational changes in the DNA repair kinase DNA-PKcs Article · 3 Nov 2003
- Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase Article · Aug 2003
- Fast rotational matching of rigid bodies by fast Fourier transform acceleration of five degrees of freedom Article · 23 Jul 2003
- Mega-Dalton biomolecular motion captured from electron microscopy reconstructions Article · Feb 2003
- EMotion: Electron microscopy in motion Article · 2003
- Conformational flexibility of bacterial RNA polymerase Article · 19 Mar 2002
- Multi-resolution contour-based fitting of macromolecular structures Article · Mar 2002
- Using Situs for the registration of protein structures with low-resolution bead models from x-ray solution scattering Article · 17 Nov 2001
- Modeling tricks and fitting techniques for multiresolution structures Article · Sep 2001
- SOMCD: Method for evaluating protein secondary structure from UV circular dichroism spectra Article · 10 Jan 2001
- Fitting multi-resolution macromolecular structures by Fourier template convolution Article · 2001
- Reconstruction of protein form with X-ray solution scattering and a genetic algorithm Article · Jun 2000
- A Genetic Algorithm for Low Resolution Protein Structure Determination Article · 1999
- Changes in microtubule protofilament number induced by taxol binding to an easily accessible site: Internal microtubule dynamics Article · Dec 1998
- Low-resolution structures of proteins in solution retrieved from x-ray scattering with a genetic algorithm Article · Jun 1998
- Fast mixing device for time-resolved synchrotron x-ray scattering studies of radiation sensitive proteins Article · 1 Jan 1998
- A prediction of DDP IV/CD26 domain structure from a physico-chemical investigation of dipeptidyl peptidase IV (CD26) from human seminal plasma Article · Jul 1997
- Tubulin secondary structure analysis, limited proteolysis sites, and homology to FtsZ Article · 1 Jan 1996
- Pattern formation in a model for prebiotic evolution Article · Jun 1995
- Spatial dynamics of a model for prebiotic evolution Article · Mar 1995
- Preface Book / chapter · 1995
- Compartimentation in replicator models Book / chapter · 1995
- A resolution of the chemotactic wave paradox Article · Mar 1994
- Evolution of Catalytic Networks Formed by Self-Replicating Species Article · 1994
- SPATIAL PATTERNS IN A CLOSED-SYSTEM FORMED BY SELF-REPLICATIVE SPECIES Article · 1993
- Estructuras espaciales en un sistema cerrado formado por especies auto-replicativas Article · 1993
- Evaluation of secondary structure of proteins from uv circular dichroism spectra using an unsupervised learning neural network Article · 1993