Research Group

Detalle de: Molecular Modeling Group

Title	Molecular Modeling Group
Description	[EN] Computational biology lab. The work is devoted to the integration of evolutive and structural information to study the function of proteins, the simulation of dynamic processes of protein-protein and protein-ligand interaction, the development of novel "in silico" drug design systems and the generation of new quantitative methods for computational biology. [ES] Laboratorio de biología computacional. El trabajo se centra en la integración de información evolutiva y estructural para estudiar la función de las proteínas, la simulación de procesos dinámicos de interacción proteína-proteína y proteína-ligando, el desarrollo de nuevos sistemas de diseño de fármacos "in silico" y la generación de nuevos métodos cuantitativos para biología computacional.
Home Page	https://bioweb.cbm.uam.es/
Contact Email	pagomez@cbm.csic.es
Collaborating Companies	Biomol-Informatics SL (R&D contract in bioinformatics with the Fundación Severo Ochoa, 2008-2017)
Spin Off	Biomol-Informatics SL (founder, 2007) - spin-off company of the Madrid Science Park (Parque Científico de Madrid)
Patents	Soluble miniACE2 proteins that interact with SARS-CoV-2 and uses thereof (2022). Patent no. PCT/IB2023/054335 [WO/2023/209619]. In collaboration with the Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud (IDCBIS), Bogotá, Colombia.
Hpc Resources
Institution	CBM
Ontology	Computational Methods, Structural bioinformatics, Computational models and simulations, Biomolecular simulation, Structure-function relationship, Drug Discovery and design, Structure prediction, Molecular Interactions/Docking, Protein/Nucleic Acid design
Tools	MEPSA: Minimum Energy Pathway Analysis for energy landscapes., MEPSAnd: minimum energy path surface analysis over n-dimensional surfaces.
Service Units
Research Lines	Analysis by computational simulation of enzymatic reactions catalyzed by enzymes of biomedical interest. Design of specific inhibitors., Development of efficient methods for calculating paths of minimum or maximum parameter values (e.g., minimum energy paths) through surfaces of any number of dimensions., Computational analysis by molecular dynamics simulation of macromolecular complexes of biomedical interest, Development of a new and efficient drug design system based on computational dynamic simulation of macromolecular structures
Funded Projects	New drugs to inhibit Carbapenemases. Discovery of compounds by structural design (DrugCarbapenem), Bio-PARTNeR: Protein interaction network, GenomeSpace: Sequence to structure, Molecular basis of the anti-obesity properties of C75 compound, Bioinformatics: Protein-protein and protein-ligand interactions. Modeling human CPTI function, Bioinformatics: Structure and function of human CPTI, BIOSINCEL. Synthetic biology of cellular division: reconstruction of the bacterial division proto-ring, COMBACT-CM. New targets to combat pathogenic bacteria, Molecular bases of action of carnitine palmitoyltransferases as regulators of fat oxidation and their role on insulin resistance, type II diabetes and the hypothalamic appetite regulation, DIVINOCELL. Exploiting Gram-negative cell division targets in the test tube to obtain antimicrobial compounds, DORIAN. Developmental origins of healthy and unhealthy ageing: the role of maternal obesity, Use of specific peptides from proteins FtsA and FtsZ as antimicrobials, DIGEN-1K: Experimental development of a Genetic Diagnostics Method using Next Generation Sequencing, COMPUDRUG: Development of a new and efficient drug design system based on computational dynamic calculation of macromolecular structures, CONNECT: inCreasing cOmmunicatioN, awareNEss and data sharing in a global approaCh against resisTance, DRUGCOHESIN: New drugs for chromosome biology. Design of specific inhibitors of the Cohesin complex, EPIC Alliance: Alliance for the Exploration of Pipelines for Inhibitors of Carbapenemases, Combating Antibiotic-Resistant Enterobacteriaceae (CARE): structure-based discovery of clinical trial-ready inhibitors, Drug design through computational screening with implications for rare diseases, cancer and fertility, Contract for Research and Development on Bioinformatics between Biomol-Informatics SL and Fundación Severo Ochoa
Selected Publications	Biallelic loss-of-function variants in ZNF142 are associated with a robust DNA methylation signature affecting a limited number of genomic loci Article · 23 May 2025 An engineered miniACE2 protein secreted by mesenchymal stromal cells effectively neutralizes multiple SARS-CoV- 2 variants in vitro Article · 23 Apr 2025 Structural Basis for Alternative Self-Assembly Pathways Leading to Different Human Immunodeficiency Virus Capsid-Like Nanoparticles Article · 27 Sep 2024 STAG2-RAD21 complex: A unidirectional DNA ratchet mechanism in loop extrusion Article · Sep 2024 The phenotypic and genotypic spectrum of individuals with mono‐ or biallelic ANK3 variants Article · 11 Jul 2024 View all (127 more) Pathogenic effects of Leu200Pro and Arg387His VRK1 protein variants on phosphorylation targets and H4K16 acetylation in distal hereditary motor neuropathy Article · 30 Mar 2024 STAG2: Computational Analysis of Missense Variants Involved in Disease Article · 20 Jan 2024 Distinct GSDMB protein isoforms and protease cleavage processes differentially control pyroptotic cell death and mitochondrial damage in cancer cells Article · 11 Mar 2023 Computational Modeling and Design of New Inhibitors of Carbapenemases: A Discussion from the EPIC Alliance Network Article · 28 Aug 2022 Molecular Basis of the Schuurs–Hoeijmakers Syndrome: What We Know about the Gene and the PACS-1 Protein and Novel Therapeutic Approaches Article · 25 Aug 2022 A Novel Intragenic Duplication in the HDAC8 Gene Underlying a Case of Cornelia de Lange Syndrome Article · 8 Aug 2022 Biallelic variants in ZNF142 lead to a syndromic neurodevelopmental disorder Article · 8 Jun 2022 Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase Article · 27 Apr 2022 Neurodevelopmental Disorders Associated with PSD-95 and Its Interaction Partners Article · 15 Apr 2022 CIBERER: Spanish national network for research on rare diseases: A highly productive collaborative initiative Article · 4 Feb 2022 The clinical and molecular spectrum of QRICH1 associated neurodevelopmental disorder Article · 11 Dec 2021 Things are not always what they seem: From Cornelia de Lange to KBG phenotype in a girl with genetic variants in NIPBL and ANKRD11 Article · 7 Oct 2021 Dysfunctional Homozygous VRK1-D263G Variant Impairs the Assembly of Cajal Bodies and DNA Damage Response in Hereditary Spastic Paraplegia Article · Oct 2021 Clinical relevance of postzygotic mosaicism in Cornelia de Lange syndrome and purifying selection of NIPBL variants in blood Article · 29 Jul 2021 DLG4-related synaptopathy: a new rare brain disorder Article · May 2021 Pathogenic convergence of CNVs in genes functionally associated to a severe neuromotor developmental delay syndrome Article · 8 Feb 2021 Novel Dominant KCNQ2 Exon 7 Partial In-Frame Duplication in a Complex Epileptic and Neurodevelopmental Delay Syndrome Article · 23 Jun 2020 VRK1 (Y213H) homozygous mutant impairs Cajal bodies in a hereditary case of distal motor neuropathy Article · May 2020 Delineation of phenotypes and genotypes related to cohesin structural protein RAD21 Article · 19 Mar 2020 Evaluating Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes Article · 4 Feb 2020 More Than One HMG-CoA Lyase: The Classical Mitochondrial Enzyme Plus the Peroxisomal and the Cytosolic Ones Article · 4 Dec 2019 MEPSAnd: minimum energy path surface analysis over n-dimensional surfaces Software · 16 Aug 2019 A novel RAD21 p.(Gln592del) variant expands the clinical description of Cornelia de Lange syndrome type 4 – Review of the literature Article · Jun 2019 Identification of temperature-sensitive mutations and characterization of thermolabile RNase II variants Article · 28 Dec 2018 Population structure of OXA-48-producing Klebsiella pneumoniae ST405 isolates during a hospital outbreak characterised by genomic typing. Article · Dec 2018 Human Mitochondrial HMG-CoA Synthase Deficiency: Role of Enzyme Dimerization Surface and Characterization of Three New Patients Article · 28 Mar 2018 Two-step ATP-driven opening of cohesin head Article · 12 Jun 2017 A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases Article · 1 Jun 2017 mRNA Quantification of NIPBL Isoforms A and B in Adult and Fetal Human Tissues, and a Potentially Pathological Variant Affecting Only Isoform A in Two Patients with Cornelia de Lange Syndrome Article · 23 Feb 2017 Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer Article · 25 Oct 2016 In vivo functional and molecular characterization of the Penicillin-Binding Protein 4 (DacB) of Pseudomonas aeruginosa Article · 6 Oct 2016 Special Cases in Cornelia de Lange Syndrome: The Spanish Experience Article · 10 May 2016 The Cell Division Protein FtsZ from Streptococcus pneumoniae Exhibits a GTPase Activity Delay Article · Oct 2015 Modulating the RNA Processing and Decay by the Exosome: Altering Rrp44/Dis3 Activity and End-Product (vol 8, e76504, 2013) Article · 21 Aug 2015 MEPSA: minimum energy pathway analysis for energy landscapes Software · 31 Jul 2015 ANISERP: a new serpin from the parasite Anisakis simplex Article · 28 Jul 2015 Comparing Molecular Dynamics Force Fields in the Essential Subspace Article · 26 Mar 2015 De Novo Heterozygous Mutations in SMC3 Cause a Range of Cornelia de Lange Syndrome-Overlapping Phenotypes Article · 17 Mar 2015 A Practical Quantum Mechanics Molecular Mechanics Method for the Dynamical Study of Reactions in Biomolecules Book / chapter · 2015 Design of clone-specific probes from genome sequences for rapid PCR-typing of outbreak pathogens Article · Nov 2014 Severe ipsilateral musculoskeletal involvement in a Cornelia de Lange patient with a novel NIPBL mutation Article · Sep 2014 Molecular basis of the association of H208Y and thymidine analogue resistance mutations M41L, L210W and T215Y in the HIV-1 reverse transcriptase of treated patients Article · Jun 2014 FIREBALL/AMBER: An Efficient Local-Orbital DFT QM/MM Method for Biomolecular Systems Article · 2 May 2014 Somatic mosaicism in a Cornelia de Lange syndrome patient with NIPBL mutation identified by different next generation sequencing approaches Article · 26 Jan 2014 Developmental ORIgins of Healthy and Unhealthy AgeiNg: The Role of Maternal Obesity - Introduction to DORIAN Article · 2014 Torsion and curvature of FtsZ filaments Article · 2014 New case of mitochondrial HMG-CoA synthase deficiency. Functional analysis of eight mutations Article · Aug 2013 Analysis of aberrant splicing and nonsense-mediated decay of the stop codon mutations c.109G > T and c.504_505delCT in 7 patients with HMG-CoA lyase deficiency Article · Apr 2013 Ddi1-like protein from Leishmania major is an active aspartyl proteinase Article · Mar 2013 Simulation of Catalytic Water Activation in Mitochondrial F-1-ATPase Using a Hybrid Quantum Mechanics/Molecular Mechanics Approach: An Alternative Role for beta-Glu 188 Article · 25 Jan 2013 Genome Sequence of OXA-48 Carbapenemase-Producing Klebsiella pneumoniae KpO3210 Article · 15 Dec 2012 Mutations That Hamper Dimerization of Foot-and-Mouth Disease Virus 3A Protein Are Detrimental for Infectivity Article · 15 Oct 2012 The only exoribonuclease present in Haloferax volcanii has an unique response to temperature changes Article · Oct 2012 Characterization of a novel HMG-CoA lyase enzyme with a dual location in endoplasmic reticulum and cytosol Article · Oct 2012 Surface-Enhanced Raman Scattering-Based Detection of the Interactions between the Essential Cell Division FtsZ Protein and Bacterial Membrane Elements Article · 27 Jul 2012 Molecular dynamics simulation of GTPase activity in polymers of the cell division protein FtsZ Article · 28 Mar 2012 Molecular dynamics analysis of conformational change of paramyxovirus F protein during the initial steps of membrane fusion Article · Mar 2012 The role of Gln(61) in HRas GTP hydrolysis: a quantum mechanics/molecular mechanics study (vol 102, pg 152, 2012 ) Article · Mar 2012 The Role of GIn(61) in HRas GTP Hydrolysis: A Quantum Mechanics/Molecular Mechanics Study Article · Jan 2012 Characterization of splice variants of the genes encoding human mitochondrial HMG-CoA lyase and HMG-CoA synthase, the main enzymes of the ketogenesis pathway Article · 28 Sep 2011 Swapping the domains of exoribonucleases RNase II and RNase R: Conferring upon RNase II the ability to degrade ds RNA Article · 4 Apr 2011 Nanomechanics of the Cadherin Ectodomain "CANALIZATION" BYCa2 BINDING RESULTS IN A NEW MECHANICAL ELEMENT Article · Mar 2011 Technical phosphoproteomic and bioinformatic tools useful in cancer research. Article · 2011 The African swine fever virus lectin EP153R modulates the surface membrane expression of MHC class I antigens Article · 11 Nov 2010 Neutralization of Human Respiratory Syncytial Virus Infectivity by Antibodies and Low-Molecular-Weight Compounds Targeted against the Fusion Glycoprotein Article · 15 Aug 2010 Strong FtsZ is with the force: mechanisms to constrict bacteria Article · Aug 2010 CDKN1C (p57(Kip2)) Analysis in Beckwith-Wiedemann Syndrome (BWS) Patients: Genotype-Phenotype Correlations, Novel Mutations, and Polymorphisms Article · 14 May 2010 Mutations and Variants in the Cohesion Factor Genes NIPBL, SMC1A, and SMC3 in a Cohort of 30 Unrelated Patients With Cornelia de Lange Syndrome Article · 26 Mar 2010 Structural and Functional Model for Ionic (K+/Na+) and pH Dependence of GTPase Activity and Polymerization of FtsZ, the Prokaryotic Ortholog of Tubulin Article · Jul 2009 Determination of Key Residues for Catalysis and RNA Cleavage Specificity ONE MUTATION TURNS RNase II INTO A "SUPER-ENZYME" Article · Jul 2009 C75 is converted to C75-CoA in the hypothalamus, where it inhibits carnitine palmitoyltransferase 1 and decreases food intake and body weight Article · Mar 2009 Ten Novel HMGCL Mutations in 24 Patients of Different Origin with 3-Hydroxy-3-Methyl-Glutaric Aciduria Article · 28 Jan 2009 The structure of CCT-Hsc70(NBD) suggests a mechanism for Hsp70 delivery of substrates to the chaperonin Article · 27 Jul 2008 New insights into the mechanism of RNA degradation by ribonuclease II - Identification of the residue responsible for setting the RNase II end product Article · May 2008 Residues in human respiratory syncytial virus P protein that are essential for its activity on RNA viral synthesis Article · Mar 2008 Structural properties of the human respiratory syncytial virus P protein: Evidence for an elongated homotetrameric molecule that is the smallest orthologue within the family of paramyxovirus polymerase cofactors Article · 25 Feb 2008 An evolutionary and structure-based docking model for glucocerebrosidase-saposin C and glucocerebrosidase-substrate interactions - Relevance for Gaucher disease Article · 2 Jan 2008 Molecular genetics of HMG-CoA lyase deficiency Article · Nov 2007 Definition by functional and structural analysis of two malonyl-CoA sites in carnitine palmitoyltransferase 1A Article · Jun 2007 C-terminal end and aminoacid Lys(48) in HMG-CoA lyase are involved in substrate binding and enzyme activity Article · Jun 2007 Control of the respiratory metabolism of Thermus thermophilus by the nitrate respiration conjugative element NCE Article · 24 Apr 2007 Quasi-atomic model of bacteriophage T7 procapsid shell: Insights into the structure and evolution of a basic fold Article · Apr 2007 Ca2+ activation kinetics of the two aspartate-glutamate mitochondrial carriers, aralar and citrin - Role in the heart malate-aspartate NADH shuttle Article · Mar 2007 The role of the S1 domain in exoribonucleolytic activity: Substrate specificity and multimerization Article · 22 Jan 2007 Mutational Spectrum of Maple Syrup Urine Disease in Spain Article · Jul 2006 Mutagenesis of specific amino acids converts carnitine acetyltransferase into carnitine palmitoyltransferase Article · 25 Apr 2006 Novel effect of C75 on carnitine palmitoyltransferase I activity and palmitate oxidation Article · 14 Mar 2006 A single-residue mutation, G203E, causes 3-hydroxy-3-methylglutaric aciduria by occluding the substrate channel in the 3D structural model of HMG-CoA lyase Article · Feb 2006 Computational approaches to model ligand selectivity in drug design Article · 1 Jan 2006 Kinetic and stability analysis of PKU mutations identified in BH4-responsive patients Article · Dec 2005 Scoring docking models with evolutionary information Article · 24 Jun 2005 Skipping of exon 2 and exons 2 plus 3 of HMG-CoA lyase (HL) gene produces the loss of beta sheets 1 and 2 in the recently proposed (beta-alpha)(8) TIM Barrel model of HL Article · Apr 2005 Redesign of carnitine acetyltransferase specificity by protein engineering Article · Aug 2004 TRAF family proteins link PKR with NF-kappa B activation Article · 1 May 2004 Structural model of carnitine palmitoyltransferase I based on the carnitine acetyltransferase crystal Article · 1 May 2004 The substrate recognition mechanisms in chaperonins Article · 25 Feb 2004 Sequence and structural alignments of eukaryotic and prokaryotic cytoskeletal proteins Book / chapter · 2004 Bacterial morphogenes Book / chapter · 2004 Expression of porcine CD163 on monocytes/macrophages correlates with permissiveness to African swine fever infection Article · 1 Dec 2003 A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae Article · Nov 2003 Structural (beta alpha)(8) TIM barrel model of 3-hydroxy-3-methylglutaryl-coenzyme A lyase Article · Aug 2003 Identification of conserved amino acid residues in rat liver carnitine palmitoyltransferase I critical for malonyl-CoA inhibition - Mutation of methionine 593 abolishes malonyl-CoA inhibition Article · Mar 2003 ESF Programme on 'Integrated Approaches for Functional Genomics' Workshop on 'Modelling of Molecular Networks'. Article · Feb 2003 Phage-display and correlated mutations identify an essential region of subdomain 1C involved in homodimerization of Escherichia coli FtsA Article · 11 Dec 2002 Structure of eukaryotic prefoldin and of its complexes with unfolded actin and the cytosolic chaperonin CCT Article · 1 Dec 2002 Structure and function of a protein folding machine: the eukaryotic cytosolic chaperonin CCT Article · 13 Aug 2002 Structural model of a malonyl-CoA-binding site of carnitine octanoyltransferase and carnitine palmitoyltransferase I - Mutational analysis of a malonyl-CoA affinity domain Article · Mar 2002 Structural model of the catalytic core of carnitine palmitoyltransferase I and carnitine octanoyltransferase (COT) - Mutation of CPT I histidine 473 and alanine 381 and COT alanine 238 impairs the catalytic activity Article · Nov 2001 Antigenic and immunogenic properties of a chimera of two immunodominant African swine fever virus proteins Article · Sep 2001 Analysis of the interaction between the eukaryotic chaperonin CCT and its substrates actin and tubulin Article · Aug 2001 Escherichia coli FtsZ polymers contain mostly GTP and have a high nucleotide turnover Article · Jul 2001 Influenza A virus NEP (NS2 protein) downregulates RNA synthesis of model template RNAs Article · 15 May 2001 Influenza virus matrix protein is the major driving force in virus budding Article · 15 Dec 2000 Rescue of synthetic RNAs into Thogoto and influenza A virus particles using core proteins purified from Thogoto virus Article · Mar 2000 Several protein regions contribute to determine the nuclear and cytoplasmic localization of the influenza A virus nucleoprotein Article · 1 Jan 2000 In vitro inhibition of the replication of haemorrhagic septicaemia virus (VHSV) and African swine fever virus (ASFV) by extracts from marine microalgae Article · Nov 1999 Efficient formation of influenza virus-like particles: Dependence on the expression levels of viral proteins Article · 1 Jul 1999 Blocking antibodies inhibit complete African swine fever virus neutralization Article · Jun 1997 Neutralization susceptibility of African swine fever virus is dependent on the phospholipid composition of viral particles Article · Feb 1997 High level expression of the major antigenic African swine fever virus proteins p54 and p30 in baculovirus and their potential use as diagnostic reagents Article · Feb 1997 Neutralizing antibodies to different proteins of African swine fever virus inhibit both virus attachment and internalization Article · Aug 1996 The structural protein p54 is essential for African swine fever virus viability Article · Feb 1996 IMPROVEMENT OF AFRICAN SWINE-FEVER VIRUS NEUTRALIZATION ASSAY USING RECOMBINANT VIRUSES EXPRESSING CHROMOGENIC MARKER GENES Article · Oct 1995 THE ACTIVITY OF SYNAPTOSOMAL CALCIUM CHANNELS IS INVERSELY CORRELATED WITH WORKING-MEMORY PERFORMANCE IN MEMORY-IMPAIRED, AGED RATS Article · Jan 1994 AGE-RELATED-CHANGES IN CALCIUM HOMEOSTATIC MECHANISMS IN SYNAPTOSOMES IN RELATION WITH WORKING-MEMORY DEFICIENCY Article · Sep 1993 PYRUVATE-DEHYDROGENASE DEPHOSPHORYLATION IN RAT-BRAIN SYNAPTOSOMES AND MITOCHONDRIA - EVIDENCE FOR A CALCIUM-MEDIATED EFFECT IN RESPONSE TO DEPOLARIZATION, AND VARIATIONS DUE TO AGING Article · Aug 1992 CONDITIONS RESTRICTING DEPOLARIZATION-DEPENDENT CALCIUM INFLUX IN SYNAPTOSOMES REVEAL A GRADED RESPONSE OF P96-DEPHOSPHORYLATION AND A TRANSIENT DEPHOSPHORYLATION OF P65 Article · Jun 1991
Researchers	Paulino Gomez-Puertas

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