Now showing items 1-5 of 5

    • Challenges of docking in large, flexible and promiscuous binding sites 

      Kotev, Martin; Soliva, Robert; Orozco, Modesto (Elsevier, 2016-10-15)
      Article
      Open Access
      After decades of work, the correct determination of the binding mode of a small molecule into a target protein is still a challenging problem, whose difficulty depends on: (i) the sizes of the binding site and the ligand; ...
    • Computational Prediction of HIV-1 Resistance to Protease Inhibitors 

      Hosseini, Ali; Alibés, Andreu; Noguera-Julian, Marc; Gil, Victor; Paredes, Roger; Soliva, Robert; Orozco, Modesto; Guallar, Víctor (American Chemical Society, 2016-04-15)
      Article
      Open Access
      Development of mutations in HIV-1 PR hinders the activity of antiretroviral drugs, forcing changes in drug prescription. Most resistance assessments used to date rely on expert-based rules on predefined sets of stereotypical ...
    • FragPELE: dynamic ligand growing within a binding site. A novel tool for hit-to-lead drug design 

      Pérez, Carles; Soler, Daniel; Soliva, Robert; Guallar, Víctor (American Chemical Society (ACS), 2020)
      Article
      Open Access
      The early stages of drug discovery rely on hit-to-lead programs, where initial hits undergo partial optimization to improve binding affinities for their biological target. This is an expensive and time-consuming process, ...
    • Monte Carlo simulations using PELE to identify a protein–protein inhibitor binding site and pose 

      Díaz, Lucía; Soler, Daniel; Tresadern, Gary; Buyck, Christophe; Perez-Benito, Laura; Saen-Oon, Suwipa; Guallar, Victor; Soliva, Robert (Royal Society of Chemistry (RSC), 2020-02-17)
      Article
      Open Access
      In silico binding site location and pose prediction for a molecule targeted at a large protein surface is a challenging task. We report a blind test with two peptidomimetic molecules that bind the flu virus hemagglutinin ...
    • Pushing the Limits of Computational Structure-Based Drug Design with a Cryo-EM Structure: The Ca2+ Channel α2δ-1 Subunit as a Test Case 

      Kotev, Martin; Pascual, Rosalia; Almansa, Carmen; Guallar, Victor; Soliva, Robert (American Chemical Society, 2018-07-27)
      Article
      Open Access
      Cryo-electron microscopy (cryo-EM) is emerging as a real alternative for structural elucidation. In spite of this, very few cryo-EM structures have been described so far as successful platforms for in silico drug design. ...