Now showing items 1-8 of 8

    • A multistep docking and scoring protocol for congeneric series: Implementation on kinase DFG-out type II inhibitors 

      Granadino Roldán, José M.; Garzón Ruiz, Andrés; Pasamontes Funez, Ignacio; Tomás Belenguer, María Santos; Rubio Martínez, Jaime (2018-01-17)
      Article
      Open Access
      AIM:Rescoring of docking-binding poses can significantly improve molecular docking results. Our aim was to evaluate postprocessing docking protocols in order to determine the most suitable methodology for the study of the ...
    • Assessment of the sampling performance of multiple-copy dynamics versus a unique trajectory 

      Pérez González, Juan Jesús; Tomás Belenguer, María Santos; Rubio Martínez, Jaime (2016-10-01)
      Article
      Restricted access - publisher's policy
      The goal of the present study is to ascertain the differential performance of a long molecular dynamics trajectory versus several shorter ones starting from different points in the phase space and covering the same sampling ...
    • Discovery of diverse natural products as inhibitors of SARS-CoV-2 Mpro protease through virtual screening 

      Rubio Martínez, Jaime; Jiménez Alesanco, Ana; Ceballos Laita, Laura; Ortega Alarcón, David; Vega, Sonia; Calvo, Cristina; Benítez García, Cristina; Abian, Olga; Velázquez Campoy, Adrián; Thomson, Timothy M.; Granadino Roldán, José Manuel; Gómez Gutiérrez, Patricia; Pérez González, Juan Jesús (2021-11-22)
      Article
      Restricted access - publisher's policy
      SARS-CoV-2 is a type of coronavirus responsible for the international outbreak of respiratory illness termed COVID-19 that forced the World Health Organization to declare a pandemic infectious disease situation of international ...
    • Effect of set up protocols on the accuracy of alchemical free energy calculation over a set of ACK1 inhibitors 

      Granadino, Jose Manuel; Mey, Antonia S. J. S.; Pérez González, Juan Jesús; Bosisio, Stefano; Rubio Martínez, Jaime; Michel, Julien (Public Library of Science (PLOS), 2019-03-01)
      Article
      Open Access
      Hit-to-lead virtual screening frequently relies on a cascade of computational methods that starts with rapid calculations applied to a large number of compounds and ends with more expensive computations restricted to a ...
    • Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations 

      Rubio Martínez, Jaime; Tomás Belenguer, María Santos; Pérez González, Juan Jesús (2017-11-01)
      Article
      Open Access
      In general, peptides do not exhibit a well-defined conformational profile in solution. However, despite the experimental blurred picture associated with their structure, compelling spectroscopic evidence shows that peptides ...
    • Fragment dissolved molecular dynamics: a systematic and efficient method to locate binding sites 

      Privat, Cristian; Granadino, Jose Manuel; Bonet Ruiz, Jordi; Tomás Belenguer, María Santos; Pérez González, Juan Jesús; Rubio Martínez, Jaime (Royal Society of Chemistry (RSC), 2021)
      Article
      Open Access
      Diverse computational methods to support Fragment-based drug discovery (FBDD) are available in the literature. Despite their demonstrated efficacy to support FBDD campaigns, they exhibit some drawbacks such as protein ...
    • Identification of potential small molecule binding pockets in p38a MAP kinase 

      Gómez Gutierrez, Patricia; Rubio Martínez, Jaime; Pérez González, Juan Jesús (2017-10-23)
      Article
      Open Access
      Given the essential role played by protein kinases in regulating cellular pathways, their dysregulation can result in the onset and/or progression of various human diseases. Structural analysis of diverse protein kinases ...
    • Molecular determinants for the activation/inhibition of bak protein by BH3 peptides 

      Vila Julià, Guillem; Granadino, Jose Manuel; Pérez González, Juan Jesús; Rubio Martínez, Jaime (2020-03-23)
      Article
      Open Access
      Apoptosis is a key cell death pathway in mammalian cells. Understanding this process and its regulation has been a subject of study in the last three decades. Members of the Bcl-2 family of proteins are involved in the ...