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    • Annotating Cancer-Related Variants at Protein–Protein Interface with Structure-PPi 

      Vazquez, Miguel; Pons, Tirso (Springer US, 2022)
      Capítol de llibre
      Accés restringit per política de l'editorial
      A comprehensive analysis of germline and somatic variants requires complex computational approaches that combine next-generation sequencing (NGS)-based omics data with curated annotations from public repositories. Here, ...

    • Challenges and opportunities for RISC-V architectures towards genomics-based workloads 

      Gómez Sánchez, Gonzalo; Call Barreiro, Aaron; Teruel García, Xavier; Alonso Parrilla, Lorena; Morán Castany, Ignasi; Pérez Elena, Miguel Ángel; Torrents Arenales, David; Berral García, Josep Lluís (Springer, 2023)
      Capítol de llibre
      Accés obert
      The use of large-scale supercomputing architectures is a hard requirement for scientific computing Big-Data applications. An example is genomics analytics, where millions of data transformations and tests per patient need ...

    • Mapping enzyme-substrate interactions: its potential to study the mechanism of enzymes 

      Roda, Sergi; Santiago, Gerard; Guallar, Victor (Academic Press Inc., 2020-09)
      Capítol de llibre
      Accés obert
      With the increase of the need to use more sustainable processes for the industry in our society, the modeling of enzymes has become crucial to fully comprehend their mechanism of action and use this knowledge to enhance ...

    • Metadata to Describe Genomic Information 

      Delgado, Jaime; Naro, Daniel; Llorente, Silvia; Gelpí, Josep Lluís; Royo, Romina (IOS Press, 2018)
      Capítol de llibre
      Accés obert
      Interoperable metadata is key for the management of genomic information. We propose a flexible approach that we contribute to the standardization by ISO/IEC of a new format for efficient and secure compressed storage and ...

    • Molecular Modeling in Enzyme Design, Toward In Silico Guided Directed Evolution 

      Monza, Emanuele; Acebes, Sandra; Lucas, Fátima; Guallar, Victor (Springer, 2017-02-15)
      Capítol de llibre
      Accés obert
      Directed evolution (DE) creates diversity in subsequent rounds of mutagenesis in the quest of increased protein stability, substrate binding, and catalysis. Although this technique does not require any structural/mechanistic ...

    • Monte Carlo Techniques for Drug Design: The Success Case of PELE 

      Gilabert, Joan F.; Lecina, Daniel; Estrada, Jorge; Guallar, Victor (Wiley, 2018-12-21)
      Capítol de llibre
      Accés obert
      This chapter summarizes the most representative software packages that readily allow running Monte Carlo (MC) simulations in relevant scenarios for drug design. It explores in detail the Protein Energy Landscape Exploration ...

    • Structural characterization of protein–protein interactions with pyDockSAXS 

      Jiménez-García, Brian; Bernadó, Pau; Fernández-Recio, Juan (Humana Press, 2020)
      Capítol de llibre
      Accés obert
      Structural characterization of protein–protein interactions can provide essential details to understand biological functions at the molecular level and to facilitate their manipulation for biotechnological and biomedical ...

    • Structural Prediction of Protein–Protein Interactions by Docking: Application to Biomedical Problems 

      Barradas-Bautista, Didier; Rosell, Mireia; Pallara, Chiara; Fernández-Recio, Juan (Academic Press, 2018)
      Capítol de llibre
      Accés obert
      A huge amount of genetic information is available thanks to the recent advances in sequencing technologies and the larger computational capabilities, but the interpretation of such genetic data at phenotypic level remains ...