Recent Submissions

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  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)
  Part of book or chapter of book
  Open Access

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

  Vazquez, Miguel; Pons, Tirso (Springer US, 2022)
  Part of book or chapter of book
  Open Access

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

  Roda, Sergi; Santiago, Gerard; Guallar, Victor (Academic Press Inc., 2020-09)
  Part of book or chapter of book
  Open Access

  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 ...
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  Structural characterization of protein–protein interactions with pyDockSAXS 

  Jiménez-García, Brian; Bernadó, Pau; Fernández-Recio, Juan (Humana Press, 2020)
  Part of book or chapter of book
  Open Access

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

  Gilabert, Joan F.; Lecina, Daniel; Estrada, Jorge; Guallar, Victor (Wiley, 2018-12-21)
  Part of book or chapter of book
  Open Access

  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 ...
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  Metadata to Describe Genomic Information 

  Delgado, Jaime; Naro, Daniel; Llorente, Silvia; Gelpí, Josep Lluís; Royo, Romina (IOS Press, 2018)
  Part of book or chapter of book
  Open Access

  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 ...
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  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)
  Part of book or chapter of book
  Open Access

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

  Monza, Emanuele; Acebes, Sandra; Lucas, Fátima; Guallar, Victor (Springer, 2017-02-15)
  Part of book or chapter of book
  Open Access

  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 ...