Implementation of an effective non-bonded interactions kernel for biomolecular simulations on the Cell processor. - Horacio Emilio Pérez Sánchez; Wolfgang Wenzel (GI Jahrestagung, 2009)

High throughput in-silico screening against flexible protein receptors. - Horacio Emilio Pérez Sánchez; Bernhard Fischer; Daria B. Kokh; Holger Merlitz; Wolfgang Wenzel (J. Cheminformatics, 2010)

Accelerating multiple target drug screening on GPUs. - Irene Sánchez-Linares; Horacio Emilio Pérez Sánchez; Ginés D. Guerrero; José M. Cecilia; José M. García 001 (CMSB, 2011)

A Pipeline Pilot based SOAP implementation of FlexScreen for High-Throughput Virtual Screening. - Horacio Emilio Pérez Sánchez; Ivan Kondov; José M. García 001; Konstantin V. Klenin; Wolfgang Wenzel (IWSG-Life, 2011)

Effective Parallelization of Non-bonded Interactions Kernel for Virtual Screening on GPUs. - Ginés D. Guerrero; Horacio Emilio Pérez Sánchez; Wolfgang Wenzel; José M. Cecilia; José M. García 001 (PACBB, 2011)

Accelerating Grid Kernels for Virtual Screening on Graphics Processing Units. - Irene Sánchez-Linares; Horacio Emilio Pérez Sánchez; José M. García 001 (PARCO, 2011)

Parallelization of Virtual Screening in Drug Discovery on Massively Parallel Architectures. - Ginés D. Guerrero; Horacio Emilio Pérez Sánchez; José M. Cecilia; José M. García 001 (PDP, 2012)

High-Throughput parallel blind Virtual Screening using BINDSURF. - Irene Sánchez-Linares; Horacio Emilio Pérez Sánchez; José M. Cecilia; José M. García 001 (BMC Bioinform., 2012)

Improving drug discovery using a neural networks based parallel scoring function. - Horacio Emilio Pérez Sánchez; Ginés D. Guerrero; José M. García 001; Jorge Peña-García; José M. Cecilia; Gaspar Cano; Sergio Orts-Escolano; José García Rodríguez 001 (IJCNN, 2013)

Impact of implicit solvation models on database enrichment in GPU based blind Virtual Screening. - Ginés D. Guerrero; José M. Cecilia; José M. García 001; Horacio Emilio Pérez Sánchez (IWBBIO, 2013)

A GPU based Conformational Entropy Calculation Method. - Qian Zhang 063; José M. García 001; Junmei Wang; Tingjun Hou; Horacio Emilio Pérez Sánchez (IWBBIO, 2013)

Accelerated Conformational Entropy Calculations Using Graphic Processing Units. - Qian Zhang 063; Junmei Wang; Ginés D. Guerrero; José M. Cecilia; José M. García 001; Youyong Li; Horacio Emilio Pérez Sánchez; Tingjun Hou (J. Chem. Inf. Model., 2013)

An Efficient Solvent Accessible Surface Area calculation applied in Ab Initio Protein Structure Prediction. - Daniel Rodrigo Ferraz Bonetti; Horacio Pérez Sánchez; Alexandre C. B. Delbem (IWBBIO, 2014)

Application of parallel blind docking with BINDSURF for the study of platinum derived compounds as anticancer drugs. - José Pedro Cerón-Carrasco; Javier Cerezo; Jose Zuñiga; Alberto Requena; Julia Contreras-Garcia; Sonali Chavan; Miguel Manrubia-Cobo; Baldomero Imbernon; José M. Cecilia; Horacio Emilio Pérez Sánchez (IWBBIO, 2014)

Parallel Computation of Non-Bonded Interactions in Drug Discovery: Nvidia GPUs vs. Intel Xeon Phi. - Jianbin Fang; Ana Lucia Varbanescu; Baldomero Imbernon; José M. Cecilia; Horacio Emilio Pérez Sánchez (IWBBIO, 2014)

An improved Fuzzy Clustering methodology applied to the study of Protein Conformational Ensembles. - Duhu Man; Isabel Maria Timon-Perez; Jesús A. Soto Espinosa; Antonio Flores-Sintas; José M. Cecilia; Horacio Emilio Pérez Sánchez (IWBBIO, 2014)

The role of High Performance Computing in Bioinformatics. - Horacio Emilio Pérez Sánchez; José M. Cecilia; Ivan Merelli (IWBBIO, 2014)

Optimizations to enhance sustainability of MPI applications. - Jesús Carretero 001; Javier García Blas; David E. Singh; Florin Isaila; Thomas Fahringer; Radu Prodan; George Bosilca; Alexey L. Lastovetsky; Christi Symeonidou; Horacio Emilio Pérez Sánchez; José M. Cecilia (EuroMPI/ASIA, 2014)

Improving drug discovery using hybrid softcomputing methods. - Horacio Emilio Pérez Sánchez; Gaspar Cano; José García Rodríguez 001 (Appl. Soft Comput., 2014)

Toward energy efficiency in heterogeneous processors: findings on virtual screening methods. - Ginés D. Guerrero; Juan M. Cebrian; Horacio Emilio Pérez Sánchez; José M. García 001; Manuel Ujaldon; José M. Cecilia (Concurr. Comput. Pract. Exp., 2014)

A performance/cost model for a CUDA drug discovery application on physical and public cloud infrastructures. - Ginés D. Guerrero; Richard M. Wallace; José Luis Vázquez-Poletti; José M. Cecilia; José M. García 001; Daniel Mozos; Horacio Emilio Pérez Sánchez (Concurr. Comput. Pract. Exp., 2014)

Latest advances in distributed, parallel, and graphic processing unit accelerated approaches to computational biology. - Ivan Merelli; Horacio Emilio Pérez Sánchez; Sandra Gesing; Daniele D'Agostino (Concurr. Comput. Pract. Exp., 2014)

Support Vector Machine Prediction of Drug Solubility on GPUs. - Gaspar Cano; José García Rodríguez 001; Sergio Orts-Escolano; Jorge Peña-García; Dharmendra Kumar-Yadav; Alfonso Pérez-Garrido; Horacio Pérez Sánchez (IWBBIO (2), 2015)

Improving Activity Prediction of Adenosine A2B Receptor Antagonists by Nonlinear Models. - Fahimeh Ghasemi; Alireza Mehri Dehnavi; Jorge Peña-García; Helena den-Haan; Alfonso Pérez-Garrido; Afshin Fassihi; Horacio Pérez Sánchez (IWBBIO (2), 2015)

Enhancing the Parallelization of Non-bonded Interactions Kernel for Virtual Screening on GPUs. - Baldomero Imbernon; Antonio Llanes; Jorge Peña-García; José L. Abellán; Horacio Pérez Sánchez; José M. Cecilia (IWBBIO (2), 2015)

Molecular Docking and Biological Evaluation of Functionalized benzo[h]quinolines as Colon Cancer Agents. - Ramendra Pratap; Dharmendra Kumar-Yadav; Surjeet Singh; Reeta Rai; Naresh Kumar; Han-Sup Uhm; Harpreet Singh; Horacio Pérez Sánchez (IWBBIO (2), 2015)

DIA-DB: A Web-Accessible Database for the Prediction of Diabetes Drugs. - Antonia Sánchez-Pérez; Andrés Muñoz 001; Jorge Peña-García; Helena den-Haan; Nick Bekas; Antigoni Katsikoudi; Andreas G. Tzakos; Horacio Pérez Sánchez (IWBBIO (2), 2015)

Applications of High Performance Computing in Bioinformatics, Computational Biology and Computational Chemistry. - Horacio Pérez Sánchez; Afshin Fassihi; José M. Cecilia; Hesham H. Ali; Mario Cannataro (IWBBIO (2), 2015)

Molecular Dynamics Simulations of Ligand Recognition upon Binding Antithrombin: A MM/GBSA Approach. - Xiaohua Zhang; Horacio Pérez Sánchez; Felice C. Lightstone (IWBBIO (2), 2015)

Developing science gateways for drug discovery in a grid environment. - Horacio Pérez Sánchez; Vahid Rezaei Tabar; Vitaliy Mezhuyev; Duhu Man; Jorge Peña-García; Helena den-Haan; Sandra Gesing (PeerJ Prepr., 2015)

Acceleration of MPI mechanisms for sustainable HPC applications. - Jesús Carretero 001; Javier García-Blas; David E. Singh; Florin Isaila; Alexey L. Lastovetsky; Thomas Fahringer; Radu Prodan; Peter Zangerl; Christi Symeonidou; Afshin Fassihi; Horacio Pérez Sánchez (Supercomput. Front. Innov., 2015)

Parallel Ant Colony Optimization for the HP Protein Folding Problem. - Antonio Llanes; Carlos Vélez; Antonia M. Sánchez; Horacio Emilio Pérez Sánchez; José M. Cecilia (IWBBIO, 2016)

HYDROWEB, an Online Tool for the Calculation of Hydrodynamic Properties of Macromolecules. - Horacio Emilio Pérez Sánchez; Jorge Peña-García; Helena den-Haan; Ricardo Rodríguez-Schmidt; José Pedro Cerón-Carrasco; Adriano N. Raposo; Mounira Bouarkat; Sid Ahmed Sabeur; Francisco Guillermo Díaz-Baños (IWBBIO, 2016)

Virtual Screening: A Challenge for Deep Learning. - Javier Pérez-Sianes; Horacio Pérez Sánchez; Fernando Díaz (PACBB, 2016)

Parallel implementation of fuzzy minimals clustering algorithm. - Isabel Maria Timon-Perez; Jesús A. Soto; Horacio Emilio Pérez Sánchez; José M. Cecilia (Expert Syst. Appl., 2016)

Characterization, in Vivo Evaluation, and Molecular Modeling of Different Propofol-Cyclodextrin Complexes To Assess Their Drug Delivery Potential at the Blood-Brain Barrier Level. - Sergey Shityakov; Ramin Ekhteiari Salmas; Serdar Durdagi; Ellaine Salvador; Katalin Pápai; Maria Josefa Yáñez-Gascón; Horacio Pérez Sánchez; István Puskás; Norbert Roewer; Carola Förster; Jens-Albert Broscheit (J. Chem. Inf. Model., 2016)

Parallel Desolvation Energy Term Calculation for Blind Docking on GPU Architectures. - Hocine Saadi; Nadia Nouali-Taboudjemat; Abdellatif Rahmoun; Baldomero Imbernon; Horacio Pérez Sánchez; José M. Cecilia (ICPP Workshops, 2017)

Implementation of an Efficient Blind Docking Technique on HPC Architectures for the Discovery of Allosteric Inhibitors. - Horacio Pérez Sánchez; José Pedro Cerón-Carrasco; José M. Cecilia (ICPP Workshops, 2017)

The Forex Market as an Elastic Network Model. - Antonio V. Contreras; Sergio Navarro 001; Antonio Llanes; Andrés Muñoz 001; Horacio Pérez Sánchez; José M. Cecilia (Intelligent Environments, 2017)

Automatic selection of molecular descriptors using random forest: Application to drug discovery. - Gaspar Cano; José García Rodríguez 001; Alberto Garcia-Garcia; Horacio Pérez Sánchez; Jón Atli Benediktsson; Anil Thapa; Alastair Barr (Expert Syst. Appl., 2017)

The role of different sampling methods in improving biological activity prediction using deep belief network. - Fahimeh Ghasemi; Afshin Fassihi; Horacio Pérez Sánchez; Alireza Mehri Dehnavi (J. Comput. Chem., 2017)

Increasing Molecular Dynamics Simulations Throughput by Virtualizing Remote GPUs with rCUDA. - Javier Prades; Carlos Reaño; Federico Silla; Baldomero Imbernón; Horacio Pérez Sánchez; José M. Cecilia (ICPP Workshops, 2018)

Accelerating Drugs Discovery with Deep Reinforcement Learning: An Early Approach. - Antonio Serrano; Baldomero Imbernón; Horacio Pérez Sánchez; José M. Cecilia; Andrés Bueno-Crespo; José L. Abellán (ICPP Workshops, 2018)

Deep neural network in QSAR studies using deep belief network. - Fahimeh Ghasemi; Alireza Mehridehnavi; Afshin Fassihi; Horacio Emilio Pérez Sánchez (Appl. Soft Comput., 2018)

METADOCK: A parallel metaheuristic schema for virtual screening methods. - Baldomero Imbernón; José M. Cecilia; Horacio Emilio Pérez Sánchez; Domingo Giménez (Int. J. High Perform. Comput. Appl., 2018)

ENMX: An elastic network model to predict the FOREX market evolution. - Antonio V. Contreras; Antonio Llanes; Alberto Pérez-Bernabeu; Sergio Navarro 001; Horacio Emilio Pérez Sánchez; Jose-Juan López-Espín; José M. Cecilia (Simul. Model. Pract. Theory, 2018)

BRUSELAS: HPC Generic and Customizable Software Architecture for 3D Ligand-Based Virtual Screening of Large Molecular Databases. - Antonio-Jesús Banegas-Luna; José Pedro Cerón-Carrasco; Savíns Puertas-Martín; Horacio Pérez Sánchez (J. Chem. Inf. Model., 2019)

A methodology for evaluating multi-objective evolutionary feature selection for classification in the context of virtual screening. - Fernando Jiménez; Horacio Emilio Pérez Sánchez; José T. Palma; Gracia Sánchez; Carlos Martínez (Soft Comput., 2019)

QN-Docking: An innovative molecular docking methodology based on Q-Networks. - Antonio Serrano; Baldomero Imbernón; Horacio Pérez Sánchez; José M. Cecilia; Andrés Bueno-Crespo; José L. Abellán (Appl. Soft Comput., 2020)

When will the mist clear? On the Interpretability of Machine Learning for Medical Applications: a survey. - Antonio-Jesús Banegas-Luna; Jorge Peña-García; Adrian Iftene; Fiorella Guadagni; Patrizia Ferroni; Noemi Scarpato; Fabio Massimo Zanzotto; Andrés Bueno-Crespo; Horacio Pérez Sánchez (CoRR, 2020)

Maximizing resource usage in multifold molecular dynamics with rCUDA. - Javier Prades; Baldomero Imbernón; Carlos Reaño; Jorge Peña-García; José Pedro Cerón-Carrasco; Federico Silla; Horacio Pérez Sánchez (Int. J. High Perform. Comput. Appl., 2020)

Optimizing Electrostatic Similarity for Virtual Screening: A New Methodology. - Savíns Puertas-Martín; Juana López Redondo; Horacio Emilio Pérez Sánchez; Pilar M. Ortigosa (Informatica, 2020)

Current Status of Carbohydrates Information in the Protein Data Bank. - João L. de Meirelles; Felipe C. Nepomuceno; Jorge Peña-García; Ricardo Rodríguez-Schmidt; Horacio Pérez Sánchez; Hugo Verli (J. Chem. Inf. Model., 2020)

DIA-DB: A Database and Web Server for the Prediction of Diabetes Drugs. - Horacio Pérez Sánchez; Helena den-Haan; Jorge Peña-García; Jesús Lozano-Sánchez; María Encarnación Martínez Moreno; Antonia Sánchez-Pérez; Andrés Muñoz 001; Pedro Ruiz-Espinosa; Andreia S. P. Pereira; Antigoni Katsikoudi; José Antonio Gabaldón Hernández; Ivana Stojanovic; et al. (J. Chem. Inf. Model., 2020)

Efficient GPU-based parallelization of solvation calculation for the blind docking problem. - Hocine Saadi; Nadia Nouali-Taboudjemat; Abdellatif Rahmoun; Baldomero Imbernon; Horacio Emilio Pérez Sánchez; José M. Cecilia (J. Supercomput., 2020)

METADOCK 2: a high-throughput parallel metaheuristic scheme for molecular docking. - Baldomero Imbernón; Antonio Serrano; Andrés Bueno-Crespo; José L. Abellán; Horacio Pérez Sánchez; José M. Cecilia (Bioinform., 2021)

Combined Structure and Ligand-Based Design of Selective Acetylcholinesterase Inhibitors. - Horacio Pérez Sánchez; Helena den-Haan; Alfonso Pérez-Garrido; Jorge Peña-García; Sandipan Chakraborty; Ilkay Erdogan Orhan; Fatma Sezer Senol Deniz; José Manuel Villalgordo (J. Chem. Inf. Model., 2021)

Virtual Screening Based on Electrostatic Similarity and Flexible Ligands. - Savíns Puertas-Martín; Juana López Redondo; Antonio-Jesús Banegas-Luna; Ester M. Garzón; Horacio Emilio Pérez Sánchez; Valerie J. Gillet; Pilar M. Ortigosa (ICCSA (Workshops 2), 2022)

Increasing the Accuracy of Optipharm's Virtual Screening Predictions by Implementing Molecular Flexibility. - Savíns Puertas-Martín; Juana López Redondo; Ester M. Garzón; Horacio Pérez Sánchez; Pilar M. Ortigosa (IWBBIO (2), 2022)

Accelerating Big Data Analysis through LASSO-Random Forest Algorithm in QSAR Studies. - Fahimeh Motamedi; Horacio Pérez Sánchez; Alireza Mehridehnavi; Afshin Fassihi; Fahimeh Ghasemi (Bioinform., 2022)

SIBILA: High-performance computing and interpretable machine learning join efforts toward personalised medicine in a novel decision-making tool. - Antonio-Jesús Banegas-Luna; Horacio Pérez Sánchez (CoRR, 2022)

MultiPharm-DT: A Multi-Objective Decision Tool for Ligand-Based Virtual Screening Problems. - Savíns Puertas-Martín; Juana López Redondo; Miriam R. Ferrández; Horacio Pérez Sánchez; Pilar M. Ortigosa (Informatica, 2022)

Fighting the disagreement in Explainable Machine Learning with consensus. - Antonio-Jesús Banegas-Luna; Carlos Martinez-Cortes; Horacio Pérez Sánchez (CoRR, 2023)

ALMERIA: Boosting Pairwise Molecular Contrasts with Scalable Methods. - Rafael Mena Yedra; Juana López Redondo; Horacio Emilio Pérez Sánchez; Pilar Martínez Ortigosa (Informatica, 2024)

ESSENCE-Dock: A Consensus-Based Approach to Enhance Virtual Screening Enrichment in Drug Discovery. - Jochem Nelen; Miguel Carmena-Bargueño; Carlos Martinez-Cortes; Alejandro Rodríguez-Martínez; José Manuel Villalgordo-Soto; Horacio Pérez Sánchez (J. Chem. Inf. Model., 2024)

Global and Local Interpretable Machine Learning Allow Early Prediction of Unscheduled Hospital Readmission. - Rafael Ruiz de San Martín; Catalina Morales-Hernández; Carmen Barberá; Carlos Martinez-Cortes; Antonio-Jesús Banegas-Luna; Francisco José Segura-Méndez; Horacio Pérez Sánchez; Isabel Morales-Moreno; Juan José Hernández Morante (Mach. Learn. Knowl. Extr., 2024)

Performance Impact of Containerized METADOCK 2 on Heterogeneous Platforms. - Antonio-Jesús Banegas-Luna; Baldomero Imbernón Tudela; Carlos Martinez-Cortes; José Maria Cecilia; Horacio Pérez Sánchez (CoRR, 2025)

WISCA: A Consensus-Based Approach to Harmonizing Interpretability in Tabular Datasets. - Antonio-Jesús Banegas-Luna; Horacio Emilio Pérez Sánchez; Carlos Martinez-Cortes (CoRR, 2025)

Matched pairs demonstrate robustness against inter-assay variability. - Jochem Nelen; Horacio Pérez Sánchez; Hans De Winter; Dries Van Rompaey (J. Cheminformatics, 2025)