bioweb: molecular modeling group / grupo de modelado molecular

http://www.cbm.csic.es/bioweb

 

Íñigo Marcos Alcalde
(Santander. 1987)
Post-doc researcher / Investigador post-doctoral.
Assistant teacher / Profesor asociado UFV.

Centro de Biología Molecular "Severo Ochoa".
C/ Nicolás Cabrera, 1.
Campus UAM. Cantoblanco, 28049 Madrid. Spain.
Tel: (+34) 91-196-4662   Fax: (+34) 91-196-4420
e-mail: imarcos@cbm.csic.es
URL: http://www.cbm.csic.es/bioweb

Academic degrees / Títulos académicos
    2008. B. Sc. in Biotechnology / Diplomado en Biotecnología (Universidad Francisco de Vitoria, Madrid).
    2010. M. Sc. in Biotechnology / Licenciado en Biotecnología (Universidad Francisco de Vitoria, Madrid).
    2010. Specialist in Management of Biotechnology Companies / Especialista en Gestión de Empresas Biotecnológicas (UFV, Madrid).
    2011. Postgraduate Master in Biophysics / Máster Universitario en Biofísica (Universidad Autónoma de Madrid).
    2018. Ph.D. Biophysics / Doctor en Biofísica (Universidad Autónoma de Madrid).
Career / Trayectoria profesional.
    2010. PhD student at the Molecular Modeling Group - CBMSO (Madrid) / Estudiante de doctorado en el Grupo de Modelado Molecular - CBMSO (Madrid).
    2010-2016 Pre-doctoral fellowship. "Severo Ochoa" Foundation / Beca predoctoral. Fundación "Severo Ochoa".
    2016-date Assistant teacher / Profesor asociado. Universidad Francisco de Vitoria (Madrid).
    2018-date Post-doctoral. Molecular Modeling Group - CBMSO (Madrid).
Participation in R&D contracts and R&D proyectos / Participación en contratos de I+D y proyectos de I+D.
  • 2010. Análisis del mecanismo molecular de la regulación de MHC-I por ERK5 en linfocitos T transformados. IGMM (Institut de Génétique Moléculaire de Montpellier). PI: Dr. Martín Villalba González.
  • 2010-2012. Contract for Research and Development on Bioinformatics between Biomol-Informatics SL and Fundación "Severo Ochoa". / Contrato de Investigación y Desarrollo en Bioinformática entre Biomol-Informatics SL y la Fundación "Severo Ochoa". (Coordinador: Paulino Gómez-Puertas).
  • 2018-2021. "COMPUDRUG: Development of a new and efficient drug design system based on computational dynamic calculation of macromolecular structures". State Research Agency - Ref: RTC-2017-6494-1. (Principal Inv.: Paulino Gómez-Puertas).
  • 2018-2020. "CONNECT: inCreasing cOmmunicatioN, awareNEss and data sharing in a global approaCh against resisTance". JPIAMR Virtual Research Institute Network. (Coord: Dr. Nicola Petrosillo, INMI-Rome; Principal Inv.: Paulino Gómez-Puertas).
  • 2019-2022. "DRUGCOHESIN: New drugs for chromosome biology. Design of specific inhibitors of the Cohesin complex". State Research Agency - Ref: RTI2018-094434-B-I00. (Principal Inv.: Paulino Gómez-Puertas).
  • 2020-2023. "EPIC Alliance: Alliance for the Exploration of Pipelines for Inhibitors of Carbapenemases". Joint Programming Initiative On Antimicrobial Resistance - JPIAMR Network Plus 2020. (Coord: Dr. Elias Dahdouh, IdiPAZ-Madrid; Principal Inv.: Paulino Gómez-Puertas).
  • 2021-2023. "Combating Antibiotic-Resistant Enterobacteriaceae (CARE): structure-based discovery of clinical trial-ready inhibitors". Carlos III Health Institute - Ref: DTS20-00024. (Principal Inv.: Paulino Gómez-Puertas).
  • 2022-2025. "New drugs to inhibit Carbapenemases. Discovery of compounds by structural design (DrugCarbapenem)". State Research Agency - Ref: PID2021-126625OB-I00. (Principal Inv.: Paulino Gómez-Puertas).
Publications / Publicaciones [ PubMed ] [ ORCID 0000-0002-0674-6423 ]
(A: article/artículo; R: review/revisión; C: book chapter/capítulo de libro; O: other/otros)

 2022:
 
21(O).-
Dahdouh, E., Allander, L., Falgenhauer, L., Iorga, B.I., Lorenzetti, S., Marcos-Alcalde, I., Martin, N.I., Martínez-Martínez, L., Mingorance, J., Naas, T., Rubin, J.E., Spyrakis, F., Tängdén, T., & Gómez-Puertas, P. (2022). Computational Modeling and Design of new Inhibitors of Carbapenemases. A discussion from the EPIC Alliance network. International Journal of Molecular Sciences, in press.
20(A).-
Fernández-Justel, D., Marcos-Alcalde, I., Abascal, F., Vidaña, N., Gómez-Puertas, P., Revuelta, J.L. & Buey, R.M. (2022). Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase. Protein Science 31, e4314.  [PubMed]  [PDF]  [https://doi.org/10.1002/pro.4314]
19(A).-
Kumble, S., ..., Gómez-Puertas, P., ..., Marcos-Alcalde, I., ..., Tümer, Z. (2022). The clinical and molecular spectrum of QRICH1 associated neurodevelopmental disorder. Human Mutation 43, 266–282.  [PubMed]  [PDF]  [https://doi.org/10.1002/humu.24308]

 2021:
 
18(A).-
Latorre-Pellicer, A., Ascaso, A., Lucía-Campos, C., Gil-Salvador, M., Arnedo, M., Antoñanzas, R., Ayerza-Casas, A., Marcos-Alcalde, I., Gómez-Puertas, P., Ramos, F.J., Pié, J., & Puisac, B. (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. Molecular Genetics & Genomic Medicine 9, e1826.  [PubMed]  [PDF]  [https://doi.org/10.1002/mgg3.1826]
17(A).-
Morejón-García, P., Keren, B., Marcos-Alcalde, I., Gómez-Puertas, P., Mochel, F. & Lazo, P.A. (2021). Dysfunctional Homozygous VRK1-D263G variant impairs the assembly of Cajal bodies and DNA damage response in hereditary spastic paraplegia. Neurology Genetics 7, e624.  [PubMed]  [PDF]  [https://doi.org/10.1212/NXG.0000000000000624]
16(A).-
Latorre-Pellicer, A., Gil-Salvador, M., Parenti, I., Lucia-Campos, C., Trujillano, L., Marcos-Alcalde, I., Arnedo, M., Ascaso, A., Ayerza-Casas, A., Antonanzas-Perez, R., Gervasini, C., Piccione, M., Mariani, M., Weber, A., Kanber, D., Kuechler, A., Munteanu, M., Khuller, K., Bueno-Lozano, G., Puisac, B., Gómez-Puertas, P., Selicorni, A., Kaiser, F.J., Ramos, F.J. & Pie, J. (2021). Clinical relevance of postzygotic mosaicism in Cornelia de Lange syndrome and purifying selection of NIPBL variants in blood. Scientific Reports 11, 15459.  [PubMed]  [PDF]  [https://doi.org/10.1038/s41598-021-94958-z]
15(A).-
Rodríguez-Palmero, A., Boerrigter, M.M., Gómez-Andrés, D., Aldinger, K.A., Marcos-Alcalde, I., ... (77 authors) ... Gómez-Puertas, P., Aurora Pujol, A., & Tümer, Z. (2021). DLG4-related synaptopathy: A new rare brain disorder. Genetics in Medicine 23, 888–899.  [PubMed]  [PDF]  [https://doi.org/10.1038/s41436-020-01075-9]
14(A).-
García-Hernández, J.L., Corchete, L.A., Marcos-Alcalde, I., Gómez-Puertas, P., Fons, C. & Lazo, P.A. (2021). Pathogenic convergence of CNVs in genes functionally associated to a severe neuromotor developmental delay syndrome. Human Genomics 15, 11.  [PubMed]  [PDF]  [https://doi.org/10.1186/s40246-021-00309-4]

 2020:
 
13(A).-
Lazo, P.A., García, J.L., Gómez-Puertas, P., Marcos-Alcalde, I., Arjona, C., Villarroel, A., González-Sarmiento, R. & Fons, C. (2020). Novel dominant KCNQ2 exon 7 partial in-frame duplication in a complex epileptic and neurodevelopmental delay syndrome. International Journal of Molecular Sciences 21, 4447.  [PubMed]  [PDF]  [https://doi.org/10.3390/ijms21124447]
12(A).-
Marcos, A.T., Martín-Doncel, E., Morejón-García, P., Marcos-Alcalde, I., Gómez-Puertas, P., Segura-Puimedon, M., Armengol, L., Navarro-Pando, J.M. & Lazo, P.A. (2020). VRK1 (Y213H) homozygous mutant impairs Cajal bodies in a hereditary case of distal motor neuropathy. Annals of Clinical and Translational Neurology 7, 808-818.  [PubMed]  [PDF]  [Suppl. Mat. PDF]  [https://doi.org/10.1002/acn3.51050]
11(A).-
Marcos-Alcalde, I., Lopez-Viñas, E. & Gómez-Puertas, P. (2020). MEPSAnd: Minimum Energy Path Surface Analysis over n-dimensional surfaces. Bioinformatics 36, 956–958.  [PubMed]  [Free-access article link]  [https://doi.org/10.1093/bioinformatics/btz649]
10(R).-
Krab, L.C., Marcos-Alcalde, I., Assaf, M., Balasubramanian, M., Andersen, J.B., Pedersen, A-M.B., Cefle, K., Fitzpatrick, D., Gudmundsson, S., Huisman, S., McKee, S., Maas, S.M., Menke, L.A., Mulder, P.A., Martínez, F., Mokry, J., Murch, O.D., Parker, M., Pie, J., Ramos, F., Rieubland, C., Scarano, E., Shinawi, M., Gómez-Puertas, P., Tümer, Z. & Hennekam, R.C. (2020). Delineation of phenotypes related to cohesin structural protein RAD21. Human Genetics 139, 575–592.  [PubMed]  [PDF]  [Suppl. Mat. PDF]  [https://doi.org/10.1007/s00439-020-02138-2]
9(A).-
Latorre-Pellicer, A., Ascaso, A., Trujillano, L., Gil-Salvador, M., Arnedo, M., Lucia-Campos, C., Antoñanzas-Pérez, R., Marcos-Alcalde, I., Parenti, I., Bueno-Lozano, G., Musio, A., Puisac, B., Kaiser, F.J., Ramos, F.J., *Gómez-Puertas, P. & *Pié, J. (*Corresponding authors) (2020). Evaluating Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes. International Journal of Molecular Sciences 21, 1042.  [PubMed]  [PDF]  [https://doi.org/10.3390/ijms21031042]

 2019:
 
8(A).-
Gudmundsson, S., Annéren, G., Marcos-Alcalde, I., Wilbe, M., Melin, M., Gómez-Puertas, P. & Bondeson, M-L. (2019). A novel RAD21 p.(Gln592del) variant expands the clinical description of Cornelia de Lange syndrome type 4 - review of the literature. European Journal of Medical Genetics 62, 103526.  [PubMed]  [PDF]  [https://doi.org/10.1016/j.ejmg.2018.08.007]

 2018:
 
7(A).-
*Puisac, B., *Marcos-Alcalde, I., Hernández-Marcos, M., Tobajas, P., Levtova, A., Schwahn, B.C., DeLaet, C., Lace, B., **Gómez-Puertas, P. & **Pié, J. (*Co-first-authors. **Corresponding authors). (2018). Human mitochondrial HMG-CoA synthase deficiency: role of enzyme dimerization surface and characterization of three new patients. International Journal of Molecular Sciences 19, 1010.  [PubMed]  [PDF]  [https://doi.org/10.3390/ijms19041010]

 2017:
 
6(A).-
Marcos-Alcalde, I., Mendieta-Moreno, J.I., Puisac, B., Gil-Rodríguez, M.C., Hernández-Marcos, M., Soler-Polo, D., Ramos, F.J., Ortega, J., Pié, J., Mendieta, J. & Gómez-Puertas, P. (2017). Two-step ATP-driven opening of cohesin head. Scientific Reports 7, 3266.  [PubMed]  [PDF]  [https://doi.org/10.1038/s41598-017-03118-9]
5(A).-
Buey, R.M., Fernández-Justel, D., Marcos-Alcalde. Í., Winter, G., Gómez-Puertas, P., de Pereda, J.M. & Revuelta, J.L. (2017). A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases. Scientific Reports 7, 2648.  [PubMed]  [PDF]  [https://doi.org/10.1038/s41598-017-02805-x]

 2015:
 
4(A).-
Marcos-Alcalde, I., Setoain, J., Mendieta-Moreno, J.I., Mendieta, J. & Gómez-Puertas, P. (2015). MEPSA: minimum energy pathway analysis for energy landscapes. Bioinformatics 31, 3853-3855.  [PubMed]  [PDF]  [https://doi.org/10.1093/bioinformatics/btv453]
3(A).-
Mendieta-Moreno, J.I., Marcos-Alcalde, I., Trabada, D.G., Gómez-Puertas, P., Ortega, J. & Mendieta, J. (2015). A practical Quantum Mechanics Molecular Mechanics method for the dynamical study of reactions in biomolecules. Advances in Protein Chemistry and Structural Biology 100, 67-88.  [PubMed]  [PDF]  [https://doi.org/10.1016/bs.apcsb.2015.06.003]
2(A).-
Gil-Rodríguez, M.C., ... , Marcos-Alcalde, I., Wesselink, J-J., Lusa-Bernal, S., ... , Gómez-Puertas, P., ..., & Pié, J. (2015). De novo Heterozygous Mutations in SMC3 Cause a Range of Cornelia De Lange Syndrome-Overlapping Phenotypes. Human Mutation 36, 454-462.  [PubMed]  [PDF]  [https://doi.org/10.1002/humu.22761]

 2013:
 
1(A).-
Martín-García, F., Mendieta-Moreno, J.I., Marcos-Alcalde, I, *Gómez-Puertas, P. & Mendieta, J. (* Corresponding author). (2013). Simulation of catalytic water activation in mitochondrial F1-ATPase using a hybrid quantum mechanics/molecular mechanics approach: An alternative role for ß-Glu 188. Biochemistry 52, 959-966.  [PubMed]  [PDF]  [Supp. Inf. PDF]  [Supp. video. AVI]  [https://doi.org/10.1021/bi301109x]

Lectures given / Conferencias impartidas
  • "MEPSAnd: a path-finding tool for ndimensional energy networks". Transversal inter-program seminar. CBMSO. 28-Oct-2019 Madrid (Spain).
  • "Computational drug design". IBM Systems at Barcelona Supercomputing Center. 28-May-2019 Barcelona (Spain).
  • "Computational drug design". IBM POWER9 meeting. 06-Mar-2018 Valencia (Spain).
Fellowships / Becas
  • 2010. ERASMUS. Análisis del mecanismo molecular de la regulación de MHC-I por ERK5 en linfocitos T transformados. IGMM (Institut de Génétique Moléculaire de Montpellier).
Attendance at courses and meetings / Asistencia a cursos y reuniones
  • Ciclo de conferencias: “Terapias contra el Cáncer”. Albertch Neese: “Reproductive system: new therapies”; Patrick Mahon: “Molecular biology of cancer”; Pilar Martín Duque: “Cancer gene therapy”. Universidad Francisco de Vitoria, 2006.
  • Conferencia: “Modelos animales para el estudio de enfermedades humanas”. Dra. Mirna Pérez-Moreno. Centro Nacional de Investigaciones Oncológicas, 2008.
  • Conferencia: “Cómo hacer ratones resistentes al cáncer y cómo nos ayudan en la lucha contra el cáncer”. Dr. Manuel Serrano. Centro Nacional de Investigaciones Oncológicas, 2008.
  • Congreso: III Congreso Interuniversitario de Biotecnología. Universidad de León, 2008.
  • Ciclo de conferencias: “Células madre y terapia regenerativa”. Coordinadoras: D.ª María Cascales Angosto y D.ª Flora de Pablo. Instituto de España, 2009.
BIOWEB: MOLECULAR MODELING GROUP
Centro de Biología Molecular "Severo Ochoa"
(CBMSO, CSIC-UAM)
http://www.cbm.csic.es/bioweb
C/ Nicolás Cabrera, 1. Campus UAM, Cantoblanco
28049 Madrid. Spain
Tel: (+34) 91 196 4662 / 4663
Fax: (+34) 91 196 4420
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