2021

Journals

  1. Q. Bai*, S. Liu, Y. Tian, T. Xu, A.J. Banegas-Luna, H. Pérez-Sánchez*, J. Huang, H. Liu, X. Yao, (2021), “Application advances of deep learning methods for de novo drug design and molecular dynamics simulation”, WIREs Computational Molecular Science, DOI:10.1002/wcms.1581.
  2. D. Méndez-Álvarez, V. Herrera-Mayorga, A. Juárez-Saldivar, A. Paz-González, E. Ortiz-López, D. Bandyopadhyay, H. Pérez-Sánchez, G. Rivera, (2021), “Ligand-based virtual screening, molecular docking, and molecular dynamics of eugenol analogs as potential acetylcholinesterase inhibitors with biological activity against Spodoptera frugiperda”, Molecular Diversity, DOI:10.1007/s11030-021-10312-5.
  3. F. Motamedi, H. Pérez-Sánchez, A. Mehridehnavi, A. Fassihi, F. Ghasemi, (2021), “Accelerating Big Data Quantitative Structure-Activity Prediction through LASSO-Random Forest Algorithm in QSAR Studies”, Bioinformatics, DOI:10.1093/bioinformatics/btab659.
  4. Q. Bai*, J. Ma, S. Liu, T. Xu, A.J. Banegas-Luna, H. Pérez-Sánchez*, Y. Tian, J. Huang, H. Liu, X. Yao*, (2021), “WADDAICA: a webserver for aiding protein drug design by artificial intelligence and classical algorithm”, Computational and Structural Biotechnology Journal, DOI:10.1016/j.csbj.2021.06.017.
  5. T. Castillo-Santaella, J.J. Hernandez-Morante, J. Suarez-Olmos, J. Maldonado-Valderrama, J. Peña-García, C. Martínez-Cortes, H. Pérez-Sánchez*, (2021), “Identification of the thistle milk component Silibinin(A) and Glutathione-disulphide as potential inhibitors of the pancreatic lipase: potential implications on weight loss”, Journal of Functional Foods, DOI:10.1016/j.jff.2021.104479.
  6. A.J. Banegas-Luna*, J. Peña-García, A. Iftene, F. Guadagni, P. Ferroni, N. Scarpato, F.M. Zanzotto, A. Bueno-Crespo, H. Pérez-Sánchez*, (2021), “Towards the Interpretability of Machine Learning Predictions for Medical Applications Targeting Personalised Therapies: A Cancer Case Survey”, International Journal of Molecular Sciences, DOI:10.3390/ijms22094394.
  7. J. Grzelczyk*, G. Budryn, J. Peña-García, D. Szwajgier, I. Gałązka-Czarnecka, J. Oracz, H. Pérez-Sánchez*, (2021), “Evaluation of the inhibition of monoamine oxidase A by bioactive coffee compounds protecting serotonin degradation”, Food Chemistry, DOI:10.1016/j.foodchem.2021.129108.
  8. B. Alburquerque-González, Á. Bernabé-García, M. Bernabé-García, J. Ruiz-Sanz, F.F. López-Calderón, L. Gonnelli, L. Banci, J. Peña-García, I. Luque-Fernández, F.J. Nicolás, M.L. Cayuela-Fuentes, E. Luchinat, H. Pérez-Sánchez, S. Montoro-García, P. Conesa-Zamora, (2021), “The FDA-approved antiviral raltegravir inhibits Fascin1-dependant invasion of colorectal tumor cells in vitro and in vivo”, Cancers, DOI:10.3390/cancers13040861.
  9. H. Azizian, S. Forooghian, A. Amanlou, H Pérez-Sánchez, Massoud Amanlou, (2021), “Phenothiazine as novel human superoxide dismutase modulators: discovery, optimization, and biological evaluation”, Journal of Biomolecular Structure and Dynamics, DOI:10.1080/07391102.2021.1893819.

2020

Journals

  1. B. Imbernón*, A. Serrano, A. Bueno-Crespo, J.L. Abellán, H. Pérez-Sánchez*, J. M. Cecilia*, (2020), “METADOCK 2: A high-throughput parallelmetaheuristic scheme for molecular docking”, Bioinformatics, DOI:10.1093/bioinformatics/btz958.
  2. M. Zakłos-Szyda, G. Budryn, G. Joanna, H. Pérez-Sánchez, D. Zyzelewicz, (2020), “Evaluation of Isoflavones as Bone Resorption Inhibitors upon Interactions with Receptor Activator of Nuclear Factor-κB Ligand (RANKL)”, Molecules, DOI:10.3390/molecules25010206.
  3. B. Alburquerque-González, S. Montoro-García, A. Bernabé-García, M. Bernabé-García, P. Campioni-Rodrigues, I. Luque, F.J. Nicolas, M. Luisa-Cayuela, T. Salo, H. Pérez-Sánchez*, P. Conesa-Zamora*, (2020), “New role of antidepressant imipramine as a fascin1 inhibitor in colorectal cancer cells”, Experimental and Molecular Medicine, DOI:10.1038/s12276-020-0389-x.
  4. S Montoro-García, B. Alburquerque-González, A. Bernabé-García, M. Bernabé-García, P. Campioni-Rodrigues, H. den Haan, I. Luque, F. José Nicolas, H. Pérez-Sánchez, M.L. Cayuela, T. Salo, P. Conesa-Zamora, (2020), “Novel anti-invasive properties of a Fascin1 inhibitor on colorectal cancer cells”, Journal of Molecular Medicine, DOI:10.1007/s00109-020-01877-z.
  5. J.L. Meirelles, F.C Nepomuceno, J. Peña-García, R. Rodríguez Schmidt, H. Pérez-Sánchez, H. Verli, (2020), “Current Status of Carbohydrates Information on Protein Data Bank”, Journal of Chemical Information and Modeling, DOI:10.1021/acs.jcim.9b00874.
  6. J.J. Hernández-Morante, I. Díaz-Soler, J.S. Galindo-Muñoz, H. Pérez-Sánchez, M.C. Barberá-Ortega, C. Manuel-Martínez, J.M. Morillas-Ruiz, (2020), “Moderate Weight Loss Modifies Leptin and Ghrelin Synthesis Rhythms but Not the Subjective Sensations of Appetite in Obesity Patients”, Nutrients, DOI:10.3390/nu12040916.
  7. M. Paredes-Ramos, A. Sabín-López, J. Peña-García, H. Pérez-Sánchez, J.M. López-Vilariño, M. E. Sastre de Vicente, (2020), “Computational aided acetaminophen – phthalic acid molecularly imprinted polymer design for analytical determination of known and new developed recreational drugs”, Journal of Molecular Graphics and Modelling, DOI:10.1016/j.jmgm.2020.107627.
  8. J. Grzelczyk, G. Budryn, H. Pérez-Sánchez, (2020), “Evaluation of affinity of bioactive isolates from various coffee extracts through binding with PPAR-γ with the use of isothermal titration calorimetry and docking simulation to prevent antidiabetic effects”, Journal of Thermal Analysis and Calorimetry, DOI:10.1007/s10973-020-09801-w.
  9. S. Ślusarczyk, F.S. Deniz, R. Abel, Ł. Pecio, H. Pérez-Sánchez, J.P. Cerón-Carrasco, H. den-Haan, P. Banerjee, R. Preissner, E. Krzyżak, W. Oleszek, I.E. Orhan, A. Matkowski, (2020), “Norditerpenoids with Selective Anti-Cholinesterase 3 Activity from the Roots of Perovskia atriplicifolia 4 Benth.”, International Journal of Molecular Sciences, DOI:10.3390/ijms21124475.
  10. R. González-Louzao, C. Lucas-Abellán, H. Pérez-Sánchez, J.P. Cerón-Carrasco, J.A. Gabaldón, S. López-Miranda, M.J. Yáñez-Gascón, M. Asín-Llorca, E. Núñez-Delicado, (2020), “Encapsulation of finasteride with native and modified gamma-cyclodextrins. Extensive characterization of the complexes”, International Journal of Pharmaceutics, (in press).
  11. S. Puertas-Martín, M. Paredes-Ramos, P.M. Ortigosa, J.L. Redondo, A.J. Banegas-Luna, O. Brovarets, H. Pérez-Sánchez*, (2020), “Is high performance computing a requirement for novel drug discovery and how will this impact academic efforts?”, Expert Opinion On Drug Discovery, DOI:10.1080/17460441.2020.1758664. By invitation.
  12. H. Pérez-Sánchez*, H. den-Haan, J. Peña-García, J. Lozano-Sánchez, M.E. Martínez-Moreno, A. Sánchez-Pérez, A. Muñoz, P. Ruiz-Espinosa, A.S.P. Pereira, A. Katsikoudi, J.A. Gabaldón-Hernández, I. Stojanovic8, A.S. Carretero*, A.G. Tzakos*, (2020), “DIA-DB: a database and web server for the prediction of diabetes drugs”, Journal of Chemical Information and Modeling, DOI:10.1021/acs.jcim.0c00107.
  13. J.K. Agutaya, R. Inoue, S.S. Tsie, A.T. Quitain, J. Peña-García, H. Pérez-Sánchez, M. Sasaki, T. Kida, (2020), “Metal-free synthesis of HMF from glucose using the supercritical CO2–subcritical H2O–isopropanol system”, Industrial & Engineering Chemistry Research, DOI:10.1021/acs.iecr.0c03551.
  14. A. Serrano, B. Imbernón, H. Pérez-Sánchez, J.M. Cecilia, A. Bueno-Crespo, J.L. Abellán, (2020), “QN-Docking: An innovative molecular docking methodology based on Q-Networks”, Applied Soft Computing, DOI:10.1016/j.asoc.2020.106678.
  15. F. Berat Akçešme, J. Peña-García, H. Pérez-Sánchez, N. Bešli, (2020), “Assessment of Interaction of Human OCT 1-3 Proteins and Metformin using Silico Analyses”, Acta Chmica Slovenica, (in press).
  16. M.I. Rodríguez-López, M.T. Mercader-Ros, C. Lucas-Abellán, J.A. Pellicer, A. Pérez-Garrido, H. Pérez-Sánchez, M.J. Yáñez-Gascón, J.A. Gabaldón, E. Núñez-Delicado, (2020), “Comprehensive characterization of linalool-HP-β-Cyclodextrin inclusion complexes”, Molecules, DOI:10.3390/molecules25215069.
  17. H. Pérez-Sánchez*, H. den-Haan, A. Pérez-Garrido, J. Peña-García, S. Chakraborty, I.E. Orhan*, F.S. Deniz, J.M. Villalgordo*, (2020), “Combined structure and ligand-based design of selective acetylcholinesterase inhibitors”, Journal of Chemical Information and Modeling, DOI:10.1021/acs.jcim.0c00463
  18. H. Pérez-Sánchez*, T. Kumar, G. Priya Doss, R. Rodríguez-Schmidt, J.P. Cerón-Carrasco, J. Peña-García, Z. Ye, S. Yuan, S. Günther, (2020), “Prediction and Characterization of Influenza Virus Polymerase Inhibitors Through Blind Docking and Ligand Based Virtual Screening”, Journal of Molecular Liquids, (in press).
  19. R. Abel, Q. Chen, M. Paredes-Ramos, H. Pérez-Sánchez, F. Coluzzi, M. Rocco, C. Mura, M. Simmaco, P.E. Bourne, R. Preissner, P. Banerjee, (2020), “Computational prediction of potential inhibitors of the main protease of SARS-CoV-2“, Frontiers in Chemistry, (in press).
  20. I. Terekhova*, I. Kritskiy, M. Agafonov, R. Kumeev, C. Cortes-Martínez, H. Pérez-Sánchez*, (2020), “Selective binding of cyclodextrins with leflunomide and its pharmacologically active metabolite teriflunomide”, International Journal of Molecular Sciences, (in press).
  21. N. Pradhan, N. Akhtar, B. Nath, J. Peña-García, A. Gupta, H. Pérez-Sánchez, S. Kumar, D. Manna, Debasis, (2020), “Inhibition of Immunosuppressive Indoleamine 2,3-Dioxygenase by Targeting the Heme and Apo-form”, Chemical Communications, (in press).
  22. AJ. Banegas-Luna*, J. Peña-García, A. Iftene, F. Guadagni, P. Ferroni, N. Scarpato, F.M. Zanzotto, A. Bueno-Crespo, H. Pérez-Sánchez*, (2020), “When will the mist clear? On the Interpretability of Machine Learning for Medical Applications: a survey”, arXiv:2010.00353.

2019

Journals

  1. A. Tapia-Abellán, D. Angosto-Bazarra, H. Martínez-Banaclocha, C. Torre-Minguela, J.P. Cerón-Carrasco, H. Pérez-Sánchez, J.I. Arostegui, P. Pelegrín, (2019), “MCC950 closes the active conformation of NLRP3 to an inactive state”, Nature Chemical Biology, DOI:10.1038/s41589-019-0278-6.
  2. M. Maniyazagan, S. Chakraborty, H. Pérez-Sánchez, T. Stalin, (2019), “Encapsulation of Triclosan within 2-Hydroxypropyl–β–Cyclodextrin cavity and its application in the Chemisorption of Rhodamine B dye”, Journal of Molecular Liquids, DOI:10.1016/j.molliq.2019.02.113.
  3. I.E. Orhan, F.S. Senol, S. Trædal-Henden, J.P. Cerón-Carrasco, H. den-Haan, J. Peña-Garcíac, H. Pérez-Sánchez, E. Emerce, K. Skalicka-Wozniak, (2019), “Profiling Auspicious Butyrylcholinesterase Inhibitory Activity of Two Herbal Molecules: Hyperforin and Hyuganin C”, Chemistry & Biodiversity, DOI:10.1002/cbdv.201900017.
  4. J. Zhang, Q. Bai, H. Pérez-Sánchez, S. Shang, X. An, Xiaojun Yao, (2019), “Investigation of ECD conformational transition mechanism of GLP-1R by molecular dynamics simulations and Markov State Model”, Physical Chemistry Chemical Physics, DOI:10.1039/C9CP00080A.
  5. H. Saadi, N.N. Taboudjemat, A. Rahmoun, Baldomero Imbernón, H. Pérez-Sánchez, J.M. Cecilia, (2019), “Efficient GPU-based Parallelization of Solvation Calculation for the Blind Docking Problem”, Journal of Supercomputing, DOI:10.1007/s11227-019-02834-5.
  6. J. Prades, B. Imbernón, C. Reaño, J. Peña-García, J.P. Cerón-Carrasco, F. Silla, H. Pérez-Sánchez, (2019), “Maximizing resource usage in Multi-fold Molecular Dynamics with rCUDA”, International Journal of High Performance Computing and Applications, (in press).
  7. A. Pereira, H den-Haan, J. Peña-García, M. Moreno, H. Pérez-Sánchez, Z. Apostolides, (2019), “Exploring African medicinal plants for potential anti-diabetic compounds with the DIA-DB inverse virtual screening web server”, Molecules, (in press).
  8. A.J. Banegas-Luna, J.P. Cerón-Carrasco, S. Puertas-Martin, H. Pérez-Sánchez, (2019), “BRUSELAS: HPC generic and customizable software architecture for 3D ligand-based virtual screening of large molecular databases”, Journal of Chemical Information and Modeling, DOI:10.1021/acs.jcim.9b00279.
  9. S. Puertas-Martín, J.L. Redondo, P.M. Ortigosa, H. Pérez-Sánchez, (2019), “OptiPharm: An evolutionary algorithm to compare shape similarity”, Scientific Reports, DOI:10.1038/s41598-018-37908-6.
  10. K.V. Dileep, S. Ashok, C. Remya, K.Y. Dharmendra, H. Pérez-Sánchez*, C. Sadasivan, (2019), “Indole fragments for the design of lead molecules against pancreatitis”, Journal of Biomolecular Structure and Dynamics, DOI:10.1080/07391102.2019.1567389.
  11. S. Ślusarczyk, F. Deniz, D. Wozniak, Ł Pecioc, H. Pérez-Sánchez, J.P. Cerón-Carrasco, A. Stochmal, H. den-Haan, A. Matkowski, I.E. Orhan, (2019), “Selective in vitro and in silico cholinesterase inhibitory activity of isoflavones and stilbenes from Belamcandae chinensis rhizoma”, Phytochemistry Letters, DOI:10.1016/j.phytol.2019.02.006.
  12. Y. Tauran*, J.P. Cerón-Carrasco, M. Rhimi, F. Perret, B. Kim, D. Collard, A.W. Coleman, H. Pérez-Sánchez*, (2019), “Size and Flexibility Define the Inhibition of the H3N2 Influenza Endonuclease Enzyme by Calix[n]arenes”, Antibiotics, DOI:10.3390/antibiotics8020073.
  13. C. Kandemir-Cavas, H. Pérez-Sanchez*, N. Mert-Ozupek, L. Cavas*, (2019), “In silico Analysis of Bioactive Peptides in invasive sea grass Halophila stipulacea”, Cells, DOI:10.3390/cells8060557.
  14. A..J. Banegas-Luna, J. Peña-García, J. Contreras-García, H. Pérez-Sánchez, J.P. Cerón-Carrasco, (2019), “Labelling IL-18 with alkaloids: towards the use of cytokines as carrier molecules in chemotherapy”, Theoretical Chemistry Accounts, DOI:10.1007/s00214-019-2483-5.
  15. R. Choudharya, S.K. Venkatraman, A. Chatterjee, J. Vecstaudza, M..J. Yáñez-Gascón, H. Pérez-Sánchez, J. Locs, J. Abraham, S. Swamiappan, (2019), “Biomineralization, Antibacterial Activity and Mechanical Properties of Biowaste derived Diopside Nanopowders”, Advanced Powder Technology, DOI:10.1016/j.apt.2019.06.014.
  16. J.P. González-Gutierrez, M. Hodar, F. Viscarra, P. Paillali, N. Guerra-Díaz, H. Pessoa-Mahana, J. Hernández-Morante, H. Pérez-Sánchez, I. Bermúdez, M. Reyes-Parada, P. Iturriaga-Vásquez, (2019), “Minimal structural changes determine full and partial nicotinic receptor agonist activity for nicotine analogues”, Molecules, DOI:10.3390/molecules24152684.
  17. S.M. Martínez-Sanchez, H. Pérez-Sánchez, J.A. Gabaldón, J.Abellán-Alemán, S. Montoro-García, (2019), “Multifunctional Peptides from Spanish Dry-Cured Pork Ham: Endothelial Responses and Bioinformatics Studies”, International Journal of Molecular Sciences, DOI:10.3390/ijms20174204.
  18. A. Leyva-Pérez, M.A. Rivero-Crespo, M. Tejeda-Serrano, H. Pérez-Sánchez, J.P. Cerón-Carrasco, (2019), “Intermolecular Carbonyl–Olefin Metathesis with Vinyl Ethers Catalyzed by Homogeneous and Solid Acids in Flow”, Angewandte Chemie – International Edition, DOI:10.1002/anie.201909597.
  19. A.S.P. Pereira, A.J. Banegas-Luna, J. Peña-García, H. Pérez-Sánchez*, Z. Apostolides*, (2019), “Evaluation of the anti-diabetic activity of some Common Herbs and Spices: providing new insights with Inverse Virtual Screening”, Molecules, DOI:10.3390/molecules24224030.
  20. M.G. Montalbán, S. Chakraborty, J. Peña-García, H. Verli, G. Villora, H. Pérez-Sánchez*, F. G Díaz-Baños*, (2019), “Molecular Insight into Silk Fibroin Based Delivery Vehicle for Amphiphilic Drugs: Synthesis, Characterization and Molecular Dynamics Studies”, Journal of Molecular Liquids, DOI:10.1016/j.molliq.2019.112156.
  21. Q. Bai, S. Tan, H. Pérez-Sánchez, Z. Shen, H. Liu, X. Yao, (2019), “Conformation transition of intracellular part of GCGR in complex with agonist glucagon by conventional and accelerated molecular dynamics simulations”, Frontiers in Chemistry, DOI:10.3389/fchem.2019.00851.

2018

Journals

  1. G. Budryn, J. Grzelczyk, H. Pérez-Sánchez, (2018), “Binding of red clover isoflavones to actin as a potential mechanism of anti-metastatic activity restricting the migration of cancer cells”, Molecules, DOI:10.3390/molecules23102471.
  2. A.J. Banegas-Luna, J.P. Cerón-Carrasco, H. Pérez-Sánchez, (2018), “A review of ligand-based virtual screening web tools and screening algorithms in large molecular databases in the age of big data”, Future Medicinal Chemistry, DOI:10.4155/fmc-2018-0076.
  3. J. Pérez-Sianes, H. Pérez-Sánchez, F. Díaz, (2018), “Virtual Screening meets Deep Learning”, Current Computer-Aided Drug Design, DOI:10.2174/1573409914666181018141602.
  4. A.J. Banegas-Luna, B. Imbernón, A. Llanes-Castro, A. Pérez-Garrido, J.P. Cerón-Carrasco, S. Gesing, I. Merelli, D. D’Agostino, H. Pérez-Sánchez*, (2018), “Advances in distributed computing with modern drug Discovery”, Expert Opinion On Drug Discovery, DOI:10.1080/17460441.2019.1552936. By invitation.
  5. P. Arantes, H. Pérez-Sánchez, H. Verli, (2018), “Antithrombin Conformational Modulation by D-myo-inositol 3,4,5,6-Tetrakisphosphate (TMI), a Novel Scaffold for the Development of Antithrombotic Agents”, Journal of Biomolecular Structure and Dynamics (JBSD), DOI:10.1080/07391102.2017.1407259.
  6. G. Budryn, J. Grzelczyk, A. Jaśkiewiczk, D.Żyżelewicz, H. Pérez-Sánchez, J.P. Cerón-Carrasco, (2018), “Evaluation of butyrylcholinesterase inhibitory activity by chlorogenic acids and coffee extracts assed in ITC and docking simulation models”, Food Research International, DOI:10.1016/j.foodres.2018.04.041.
  7. S.S. Azam, S. Ahmad, A.S. Akhtar, A. Wadood, H. Pérez-Sánchez, (2018), “Subtractive Genomics, Molecular Docking and Molecular Dynamics Simulation Revealed LpxC as a Potential Drug Target Against Multi-Drug Resistant Klebsiella pneumoniae”, Interdisciplinary Sciences-Computational Life Sciences, DOI:10.1007/s12539-018-0299-y.
  8. A.V. Contreras, A. Llanes, A. Pérez-Bernabeu, S. Navarro, H. Pérez-Sánchez, J.J. López-Espín, J.M. Cecilia, (2018), “ENMX: An Elastic Network Model to predict the FOREX market evolution”, Simulation Modelling Practice and Theory, DOI:10.1016/j.simpat.2018.04.008.
  9. F. Ghasemi*, A. Mehridehnavi, A. Pérez-Garrido, H. Pérez-Sánchez*, (2018), “Comprehensive Review of the Literature Dealing with Neural Network and Deep Learning Algorithms Used in QSAR Studies: Merits and Drawbacks”, Drug Discovery Today, DOI:10.1016/j.drudis.2018.06.016.
  10. A.M. Prabhu, M. Fatiha, B. Sivaraman, M. J. Yáñez-Gascón, H. Pérez-Sánchez, (2018), “Effect of natural and modified cyclodextrins on the excited state proton transfer of 7-hydroxy-4-methylcoumarin”, Journal of Molecular Liquids, (in press).
  11. I. Rodríguez-López, T. Mercader-Ros, S. López-Miranda, J.A. Pellicer, A. Pérez-Garrido, H. Pérez-Sánchez, E. Núñez-Delicado, J.A. Gabaldón, (2018), “Thorough characterization and stability of HP-βCyclodextrin thymol inclusion complexes prepared by microwave technology. A required approach to a successful application in food industry”, Journal of The Science of Food and Agriculture, DOI:10.1002/jsfa.9307.
  12. F. Jiménez*, H. Pérez-Sánchez*, J. Palma, G. Sánchez, C. Martínez, (2018), “A methodology for evaluating multi-objective evolutionary feature selection for classification in the context of virtual screening”, Soft Computing, DOI: 10.1007/s00500-018-3479-0.
  13. M.Á. Herrera-Rueda, H. Tlahuext-Romero, P. Paoli, A. Giacoman-Martínez, J.C. Almanza-Pérez, H. Pérez-Sánchez, A. Gutiérrez-Hernández, F. Chávez-Silva, E.A. Dominguez-Mendoza, S. Estrada-Soto, G. Navarrete-Vazquea, (2018), “Design, synthesis, in vitro, in vivo and in silico pharmacological characterization of antidiabetic N-Boc-L-tyrosine-based compounds”, Biomedicine & Pharmacotherapy (in press).
  14. Q. Bai, H. Pérez-Sánchez, Z. Shi, L. Li, D. Shi, H. Liu, X. Yao, (2017), “Computational studies on horseshoe shape pocket of human orexin receptor type 2 and boat conformation of suvorexant by molecular dynamics simulations”, Chemical Biology Drug Design, (in press)
  15. J.P. Cerón-Carrasco, H. Pérez-Sánchez, J. Zúñigam A. Requena, (2018), “Antibodies as Carrier Molecules: Encapsulating Anti-Inflammatory Drugs Inside Herceptine”, Journal of Physical Chemistry B, DOI:10.1021/acs.jpcb.7b10749
  16. H. Khan, M. Zafar, H. den-Haan, H. Pérez-Sánchez, M.A. Kamal, (2018), “In-silico studies of isolated phytoalkaloid against Lipoxygenase: study based on possible correlation”, Combinatorial Chemistry & High Throughput Screening, DOI: 10.2174/1386207321666180220125406.

2017

Journals

  1. A. Hussain, A. Rauf, T. Ben Hadda, S. Ahmed, J.P. Cerón-Carrasco, H. den Haan, J. Peña-García, H. Pérez-Sánchez, N. Hussain, H. Khan, U. Farooq, A. Khanh, (2017), “Sedative and muscle relaxant activities of diterpenoids from Phlomidoschema parviflorum”, Brazilian Journal of Pharmacognosy, DOI:10.1016/j.bjp.2017.07.003.
  2. S.A. Sheriff, S. Shaik Ibrahim, T. Devaki, S. Chakraborty, S. Agarwal, H. Pérez-Sánchez, (2017), “Lycopene prevents mitochondrial dysfunction during D-galactosamine/lipopolysaccharide induced fulminant hepatic failure in albino rats”, Journal of Proteome Research, DOI:10.1021/acs.jproteome.7b00176.
  3. D.K. Yadav, S., P. Sharma, S. Misra, H. Singh, R.L. Mancera, K. Kim, C. Jang, M. Kim, H. Pérez-Sánchez, E.H. Choi, S. Kumar, (2017), “Studies of the benzopyran class of selective COX-2 inhibitors using 3D-QSAR and molecular docking”, Archives of Pharmacal Research, DOI:10.1007/s12272-017-0945-7.
  4. F. Ghasemi, A.R. Mehridehnavi, A.Fassihi, H.Pérez-Sánchez, (2017), “Deep Neural Network in QSAR studies using Deep Belief Network”, Applied Soft Computing, DOI:10.1016/j.asoc.2017.09.040.
  5. A. Prabhu. M. Fatiha, N. Leila, T. Anantha, I Navarro-González, M.J. Periago, M.J. Yáñez-Gascón, H. Pérez-Sánchez, (2017), “Investigation of 3D contour map and intermolecular interaction of dopamine with β-cyclodextrin and 2-hydroxypropyl β-cyclodextrin”, Journal of Solution Chemistry, (in press).
  6. G. Budryn, I. Gałązka-Czarnecka, E. Brzozowska, J. Grzelczyk, R. Mostowski, D. Żyżelewicz, J.P. Cerón-Carrasco, H. Pérez-Sánchez, (2017), “Evaluation of estrogenic activity of red clover (Trifolium pratense L.) sprouts cultivated under different conditions by content of isoflavones, calorimetric study and molecular modelling”, Food Chemistry, DOI:10.1016/j.foodchem.2017.10.100.
  7. M. Pérez-Abril, C. Lucas-Abellán, J. Castillo-Sánchez, H. Pérez-Sánchez, J.P. Cerón-Carrasco, I. Fortea, J.A. Gabaldón, E. Núñez-Delicado, (2017), “Systematic investigation and molecular modelling of complexation between several groups of flavonoids and HP-β-cyclodextrins ”, Journal of Functional Foods, DOI:10.1016/j.jff.2017.06.052.
  8. S. Yuan, J.F. Chan*, H. den-Haan, K.K. Chik, A.J. Zhang, C.C. Chan, V.k. POON, C.C. Yip, W. Mak, Z. Zhu, Z. Zou, K. Tee, J. Cai, K. Chan, J. Peña-García, H. Pérez-Sánchez*, J.P. Cerón-Carrasco*, K. Yuen*, (2017), “Structure-based discovery of clinically approved drugs as Zika virus NS2B-NS3 protease inhibitors that potently inhibit Zika virus infection in vitro and in vivo”, Antiviral Research, DOI:10.1016/j.antiviral.2017.07.007.
  9. R. Choudharya, P.M., J. Vecstaudzac, M.J. Yáñez-Gascón, H. Pérez Sánchez, R.N., J. Locs, S. Swamiappana, (2017), “Preparation of Nanocrystalline Forsterite by Combustion of Different Fuels and their Comparative In-vitro Bioactivity, Dissolution behaviour and Antibacterial studies”, Materials Science & Engineering C-Materials for Biological Applications, DOI:10.1016/j.msec.2017.03.308.
  10. T. Suzuki*, J.P. Cerón-Carrasco, H. Tamaoki, Y. Ishigaki, R. Katoono, T. Fukushima, H. Pérez-Sánchez*, (2017), “Stereoselective encapsulation for a Triarylmethylium o,o-dimer by natural g-cyclodextrin: Origin of chiral recognition for the axially chiral dicationic guest”, Heterocycles, DOI:10.3987/COM-17-13674.
  11. A. Pérez-Garrido, F. Girón-Rodŕıguez, A. Bueno-Crespo, J. Soto, H. Pérez-Sánchez, A. Morales-Helguera, (2017), “Fuzzy clustering as rational partition method for QSAR”, Chemometrics and Intelligent Laboratory Systems, DOI:10.1016/j.chemolab.2017.04.006.
  12. O. Brovarets, I. Voiteshenko, H. Pérez-Sánchez, D.M. Hovorun, (2017), “A QM/QTAIM research under the magnifying glass of the DPT tautomerisation of the wobble mispairs involving 2-aminopurine”, New Journal of Chemistry, DOI:10.1039/C7NJ00717E.
  13. O. Brovarets, I. Voiteshenko, H. Pérez-Sánchez, D.M. Hovorun, (2017), “A QM/QTAIM detailed look at the Watson-Crick↔wobble tautomeric transformations of the 2-aminopurine·pyrimidine mispairs”, Journal of Biomolecular Structure & Dynamics, DOI:10.1080/07391102.2017.1331864.
  14. B. Imbernón, J.M. Cecilia, H. Pérez-Sánchez, D. Giménez, (2017), “METADOCK: A Parallel Metaheuristic schema for Virtual Screening methods” , International Journal of High Performance Computing Applications, DOI: 10.1177/1094342017697471.
  15. M. Yar, L. Shahzadi, A. Farooq, S.J. Imran, J.P. Cerón-Carrasco, H. den-Haan, S. Kumar, J. Peña-García, H. Pérez-Sánchez, A. Grycova, Z. Dvorak, R. Vrzal, (2017), “In vitro modulatory effects of functionalized pyrimidines and piperidine derivatives on aryl hydrocarbon receptor (AhR) and glucocorticoid receptor (GR) activities”, Bioorganic Chemistry, DOI:10.1016/j.bioorg.2017.02.013.
  16. R. Choudharya, P.M., J. Vecstaudzac, M.J. Yáñez-Gascón, H. Pérez Sánchez, R.N., J. Locs, S. Swamiappana, (2017), “Preparation of Nanocrystalline Forsterite by Combustion of Different Fuels and their Comparative In-vitro Bioactivity, Dissolution behaviour and Antibacterial studies”, Materials Science & Engineering C-Materials for Biological Applications, DOI:10.1016/j.msec.2017.03.308.
  17. D. Vashisht, A. Pandey, A. Hermenean, M.J. Yáñez-Gascón, H. Pérez-Sánchez, K.J. Kumar*, (2016), “Effect of dry heating and ionic gum on the physicochemical and release properties of starch from Dioscorea”, International Journal of Biological Macromolecules, 10.1016/j.ijbiomac.2016.11.064.
  18. G. Cano, J García-Rodríguez, A. García-García, H. Pérez-Sánchez, J. A. Benediktsson, A. Thapa, A. Barre., (2016), “Automatic Selection of Molecular Descriptors using Random Forest: Application to Drug Discovery”, Expert Systems With Applications, DOI: 10.1016/j.eswa.2016.12.008.
  19. M. Collado-González, M. G. Montalbán, J. Peña-García, H. Pérez-Sánchez, G. Víllora, F.G. Díaz Baños, (2017), “Chitosan as stabilizing agent for negatively charged nanoparticles”, Carbohydrate Polymers, DOI:10.1016/j.carbpol.2016.12.043.
  20. A. Rauf, T.B. Hadda, J.P. Cerón-Carrasco, J. Peña-García, H. Pérez-Sánchez, H. Khan, S. Bawazeer, S. Patel, M. Mubarak, Y.N. Mabkhot, (2017), “Sedative-hypnotic-like effect and molecular docking of di-naphthodiospyrol from Diospyros lotus in an animal model”. Biomedicine & Pharmacotherapy, DOI:10.1016/j.biopha.2017.01.043.

2016

Journals

  1. H. Pérez-Sánchez*, V. Rezaei, V. Mezhuyev, D. Man, J. Peña-García, H. den-Haan, S. Gesing, (2016), “Developing Science Gateways for Drug Discovery in a Grid Environment”, SpringerPlus, DOI: 10.1186/s40064-016-2914-x.
  2. D.K. Yadav, R. Rai, N. Kumar, S. Singh, S. Misra, P. Sharma, P. Shaw, H. Pérez-Sánchez, R.L. Mancera, E.H. Choi, M. Kim, R. Pratap, (2016), “New arylated benzo[h]quinolines induces anti-cancer activity by Oxidative stress-mediated DNA damage”, Nature Scientific Reports, DOI:10.1038/srep38128.
  3. S. Shityakov, R. Salmas, S. Durdagi, E. Salvador, K. Pápai, M. Yañez-Gascón, H. Pérez-Sánchez, I. Puskás, N. Roewer, C. Förster, J. Broscheit, (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”, Journal of Chemical Information and Modeling, DOI: 10.1021/acs.jcim.6b00215.
  4. O. Brovarets*, H. Pérez-Sánchez*, D.M. Hovorun, (2016), “Structural grounds for the 2-aminopurine mutagenicity: A novel insight into the old problem of the replication errors”, RSC Advances, DOI: 10.1039/C6RA17787E.
  5. V. Citro, J. Peña-García, H. den-Haan, H. Pérez-Sánchez*, R. Prete, L. Liguori, C. Cimmaruta, M.V. Cubellis*, G. Andreotti, (2016), “Identification of an allosteric binding site on human lysosomal alpha-galactosidase opens the way to new pharmacological chaperones for Fabry disease”, PLOS ONE, DOI:10.1371/journal.pone.0165463.
  6. I.E. Orhan*, N. Kucukboyaci, I. Calis, J.P. Cerón-Carrasco, H den-Haan, J. Peña-García, H. Pérez-Sánchez*, (2016), “Acetylcholinesterase inhibitory assessment of isolated constituents from Salsola grandis Freitag, Vural & Adıgüzel and molecular modeling studies on N-acetyltryptophan”, Phytochemistry Letters, (in press).
  7. O. Brovarets, H. Pérez-Sánchez, (2016), “Whether 2-aminopurine induces incorporation errors at the DNA replication? A quantum-mechanical answer on the actual biological issue”, Journal of Biomolecular Structure & Dynamics, (in press).
  8. F. Ghasemi, A. Fassihi, H. Pérez-Sánchez, A. Mehridehnavi, (2016), “The role of Different Sampling Methods in Improving Biological Activity Prediction Using Deep Belief Network”, Journal of Computational Chemistry, (in press).
  9. D.K. Yadav, R. Rai, N. Kumar, S. Singh, S. Misra, P. Sharma, P. Shaw, H. Pérez-Sánchez, R.L. Mancera, E.H. Choi, M. Kim, R. Pratap, (2016), “New arylated benzo[h]quinolines induces anti-cancer activity by Oxidative stress-mediated DNA damage”, Nature Scientific Reports, (in press).
  10. F.S. Senola, S. Ślusarczy, A. Matkowskib, A. Pérez-Garrido, F. Girón-Rodríguez, J.P. Cerón-Carrasco, H. den-Haan, J. Peña-García, H. Pérez-Sánchez*, K. Domaradzki, I.E. Orhan*, (2016), “Selective in vitro and in silico butyrylcholinesterase inhibitory activity of diterpenes and rosmarinic acid isolated from Perovskia atriplicifolia Benth. and Salvia glutinosa L.”, Phytochemistry, (in press).
  11. O. Brovarets, H. Pérez-Sánchez, (2016), “Whether the amino-imino tautomerism of 2-aminopurine is involved into its mutagenicity? Results of a thorough QM investigation”, RSC Advances, (in press).
  12. M.C. Ballesta, D. Moreno-Fernández, H. Pérez-Sánchez, M. Carvajal, (2016), “Plant plasma membrane aquaporins in natural vesicles as potential stabilizers and carriers of glucosinolates”, Colloids and Surfaces B: Biointerfaces, DOI:10.1016/j.colsurfb.2016.03.056.
  13. I. Terekhova*, R. Kumeev, G. Alper, S. Chakraborty, H. Pérez-Sánchez, E. Núñez-Delicado, (2016), “Molecular recognition of aromatic carboxylic acids by hydroxypropyl-γ-cyclodextrin: experimental and theoretical evidence”, RSC Advances, DOI: 10.1039/c6ra06340c.
  14. M. Goodarzi, H. Pérez-Sánchez, (2016), “Octanol-Water Partition Coefficient of Armchair Polyhex BN Nanotubes with Molecular Descriptors”, Russian Journal of Physical Chemistry A, (in press).
  15. V.K. Sharma, P.P. Nandekar, A. Sangamwar, H. Pérez-Sánchez, S.M. Agarwal, (2016), “Structure guided design and binding analysis of EGFR inhibiting analogues of erlotinib and AEE788 using ensemble docking, molecular dynamics and MM-GBSA”, RSC Advances, (in press).
  16. A. Hermenean*, C. Balta, A. Ardlean, C. Cotoraci, I. Navarro-González, J.M. Vegara-Meseguer, S. Chakraborty, H. Pérez-Sánchez*, (2016), “Hepatoprotective Activity of Chrysin is Mediated by Inhibition of TNF-α in Chemically Induced Acute Liver Injury: In Vivo Study and Molecular Modelling”, Experimental and Therapeutic Medicine, (in press).
  17. P. Rajathi Queen, R. Sivaraj, P. Mosae Selvakumar, F.G Díaz Baños, G. Villora, José P. Cerón-Carrasco, H. Pérez-Sánchez, Israel M.V. Enoch, (2016), “Enhanced Zn2+ Ion–Sensing By a Benzothiazole Derivative On Encapsulation in β-Cyclodextrin”, RSC Advances, DOI: 10.1039/c6ra01202g.
  18. A. Llanes, José M. Cecilia, A. Sánchez, J. M. García, M. Amos, M. Ujaldón, (2016), “Dynamic Load Balancing on Heterogeneous Clusters for Parallel Ant Colony Optimization”, Cluster Computing, DOI:10.1007/s10586-016-0534-4
  19. G. Cano, J. García-Rodríguez, S. Orts, J. Peña-García, A. Pérez-Garrido, H. Pérez-Sánchez, (2016), “Drug solubility Prediction with Support Vector Machines on Graphic Processor Units”, Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería, DOI: 10.1016/j.rimni.2015.12.001.
  20. X. Zhang, H. Pérez-Sánchez, F. Lightstone, (2016), “A Comprehensive Docking and MM/GBSA Rescoring Study of Ligand Recognition upon Binding Antithrombin”, Current Topics in Medicinal Chemistry, (in press).
  21. A. Llanes, A. Muñóz, A. Bueno-Crespo, T. García-Valverde, A. Sánchez, F. Arcas-Túnez, H. Pérez-Sánchez, J.M. Cecilia, (2016), “Soft Computing Techiniques for the Protein Folding Problem on High Performance Computing Architectures”, Current Drug Targets, DOI:10.2174/1389450117666160201114028.
  22. S. López-Miranda, A. Serrano-Martínez, P. Hernández-Sánchez, L. Guardiola, H. Pérez-Sánchez, I. Fortea, J.A. Gabaldón, E. Núñez-Delicado, (2016), “Use of cyclodextrins to recover catechin and epicatechin from red grape pomace”, Food Chemistry, (in press).

Conference proceedings

  1. J. Peña-García, A. Pérez-Garrido, A. Muñoz, H. den-Haan, B. Imbernón, J.P. Cerón-Carrasco, D. Mrozek, A. Thapa, J. Soto, A. Banegas-Luna and H. Pérez-Sánchez, (2016) “ZincFetcher: a tool for easy compound filtering from ZINC database” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).
  2. H. Pérez-Sánchez, J. Peña-García, H. den-Haan, R. Rodríguez-Schmidt, A.N. Raposo, M. Bouarkat, S.A. Sabeur and F.G. Pérez-Sánchez, (2016) “HYDROWEB, an online tool for the calculation of hydrodynamic properties of macromolecules” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).
  3. F. Girón-Rodríguez, A. Pérez-Garrido, H. Pérez-Sánchez and J. Soto, (2016), “Fuzzy vs Kmeans clustering in QSAR data partition. A comparative study” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).
  4. J. Pedro Cerón-Carrasco, J. Peña and H. Pérez-Sánchez, (2016), “Non-steroidal anti-inflammatory drugs as inhibitors of cyclooxygenases: what we have learned and what is next” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).
  5. D. Kumar-Yadav, S. Misra, P. Sharma, H. Pérez-Sánchez, H. Singh and S. Kumar, (2016), “Molecular modeling studies of thieno[3,2-c]pyran analogues as inhibitor against the anti-inflammatory target COX-2” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).
  6. A. Llanes, C. Velez, A. M. Sánchez, H. Pérez-Sánchez and José M. Cecilia, (2016), “Parallel Ant Colony Optimization for the HP Protein Folding Problem” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).
  7. J. Pérez-Sianes, H. Pérez-Sánchez and F. Díaz, (2016) “Virtual Screening: A Challenge for Deep Learning”, In PACBB16, 10th International Conference on Practical Applications of Computational Biology & Bioinformatics (accepted).
  8. S.P. Martín, J.L. Redondo, H. den-Haan, H. Pérez-Sánchez and P.M. Ortigosa, (2016) “Multiobjective based scoring function for ligand based Virtual Screening”, In: XIII Global Optimization Workshop (GOW’16) (accepted).
  9. S. Puertas Martín, H. den-Haan, J. López Redondo, H. Pérez-Sánchez and P. Martínez Ortigosa, (2016) “Multiobjective based scoring function for ligand based virtual screening” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).
  10. J. Peña-García, H. den-Haan, A. Caballero, B. Imbernón, J.P. Cerón-Carrasco, A. Vicente-Contreras, H. Pérez-Sánchez*, (2016) “GrantFinder, a web based tool for the search of research grant calls” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).
  11. R. Rodríguez-Schmidt, J. Peña-García, A. Pérez-Garrido, H. den-Haan, A. Bueno-Crespo, J.P. Cerón-Carrasco, A. Thapa, J. Atli-Benediktsson, J. Soto and H. Pérez-Sánchez*, (2016) “A hybrid machine learning and molecular modeling methodology for the prediction of novel blood anticolagulants” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).

2015

Journals

  1. I. Timón, J. Soto, H. Pérez-Sánchez, J.M. Cecilia, (2015), “Parallel Implementation of Fuzzy Minimals Clustering Algorithm”, Expert Systems with Applications (ESWA), DOI:10.1016/j.eswa.2015.11.011.
  2. J.P. Cerón-Carrasco*, H. den-Haan, J. Peña-García, J. Contreras-García, H. Pérez-Sánchez*, (2015), “Exploiting the cyclodextrins ability for antioxidants encapsulation: a computational approach to carnosol and carnosic acid embedding”, Computational and Theoretical Chemistry,DOI:10.1016/j.comptc.2015.10.028.
  3. G. Budryn, D. Zaczyńska, B. Pałecz, D. Rachwał-Rosiak, J. Oracz, S. Belica, H. den-Haan, J. Peña-García, H. Pérez-Sánchez, (2015) “ Interactions of free and encapsulated hydroxycinnamic acids and their esters from green coffee with egg ovalbumin, whey and soy protein hydrolysates”, LWT – Food Science and Technology. DOI:10.1016/j.lwt.2015.09.001.
  4. J. Carretero, J. Garcia-Blas, D. E. Singh, F. Isaila, A. Lastovetsky, T. Fahringer, R. Prodan, C. Symeonidou, G. Bosilca, A. Fassihi, H. Pérez-Sánchez, (2015), “Acceleration of MPI mechanisms for sustainable HPC applications”, Supercomputing Frontiers and Innovations, DOI: 10.14529/jsfi150202.
  5. A. Pérez-Garrido, V. Rivero-Buceta, G. Cano, S. Kumar, H. Pérez-Sánchez, M. Tejeira-Bautista, (2015), “QSAR study of adenosine A2B receptor affinity of Xanthines and deazaxanthines”, Molecular Diversity, DOI:10.1007/s11030-015-9608-0.
  6. D. Morshedi, F. Aliakbari, A.T. Marvian, A. Fassihi, F. Pan-Montojo, H. Pérez-Sánchez, (2015), “Cuminaldehyde as the major component of Cuminum cyminum, a natural aldehyde with inhibitory effect on alpha-synuclein fibrillation and cytotoxicity”, Journal of Food Science, DOI:10.1111/1750-3841.1301.
  7. D. Kalarickal Vijayan, R. Chandran, J. Cerezo, A. Fassihi, H. Pérez-Sánchez, C. Sadasivan, (2015), “A comparative studies on the inhibitory activities of selected benzoic acid derivatives against secretory phospholipase A2, a key enzyme involved in the inflammatory pathway”, Molecular Biosystems, DOI: 10.1039/C5MB00073D
  8. S. Sepehri, H. Pérez-Sánchez, A. Fassihi, (2015) “Hantzsch-Type Dihydropyridines and Biginelli-Type Tetrahydropyrimidines: a Review on the Chemotherapeutic Activities”, Journal of Pharmacy and Pharmaceutical Sciences, 18(1), 1-52.
  9. J.M. Vegara-Meseguer, H. Pérez-Sánchez, R. Araujo, F. Martín, B. Soria, (2015), “L-type Ca2+ channels and SK channels in mouse embryonic stem cells and their contribution to cell proliferation”, Journal of Membrane Biology, DOI:10.1007/s00232-015-9779-8.
  10. H. den Haan, A. Fassihi, A. Bueno-Crespo, J. Soto, J. Vegara-Meseguer, S. Montoro, H. Pérez-Sánchez, (2015) “Application of Modern Drug Discovery Techniques in the Context of Diabetes Mellitus and Atherosclerosis”, Drug Designing, 4, e125, doi:10.4172/2169-0138.1000e125
  11. A.M. Hernández-Díaz, J.M. Cecilia, M.D. García-Román (2015), “Ajuste de modelos de cortante en hormigón estructural mediante algoritmos evolutivos” Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería, doi:10.1016/j.rimni.2015.10.001.
  12. M. Hernández, B. Imbernón, J.M. Navarro, J.M. García, J.M. Cebrián, J.M. Cecilia.
    (2015). “Evaluation of the 3-D finite difference implementation of the acoustic diffusion equation model on massively parallel architectures”, Computers & Electrical Engineering 46, 190-201.

Conference proceedings

  1. J.M. García-Martínez, E.M. Garzón, J.M. Cecilia, H. Pérez-Sánchez, P.M. Ortigosa, (2015) “A GPU solution of the HP Protein Folding Problem based on UEGO” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015 (accepted).
  2. X. Zhang, H. Pérez-Sánchez, F. Lightstone, (2015) “Molecular Dynamics Simulations of Ligand Recognition upon Binding Antithrombin: A MM/GBSA Approach” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, 584-593.
  3. F. Ghasemi, A. Mehri, J. Peña-García, H. den-Haan, A. Pérez-Garrido, A. Fassihi , H. Pérez-Sánchez, (2015) “Improving activity prediction of Adenosine A2B receptor antagonists by machine learning methods” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, 635-644.
  4. G. Cano, J. García-Rodríguez, S. Orts-Escolano, D. Kumar-Yadav, A. Pérez-Garrido , H. Pérez-Sánchez, (2015) “Support Vector Machines Prediction of drug solubility on GPUs” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, 645-654.
  5. A. Sánchez-Pérez, A. Muñóz, J. Peña-García, H. den-Haan, N. Bekas, A. Katsikoudi, A. G. Tzakos, H. Pérez-Sánchez, (2015) “DIA-DB: a web-accessible database for the prediction of diabetes drugs” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, 655-663.
  6. R. Pratap, D. Kumar-Yadav, S. Singh, R. Rai, N. Kumar, H. Uhm, H. Singh, H. Pérez-Sánchez, (2015) “Molecular docking and Biological evaluation of functionalized benzo[h]quinolines as Colon cancer agents” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, 664-673.
  7. H. Pérez-Sánchez, A. Fassihi, J. M. Cecilia, H. H. Ali, M. Cannataro, (2015) “Applications of High Performance Computing in Bioinformatics, Computational Biology and Computational Chemistry” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, 527-541.
  8. B. Imbernón, A. Llanes, J. Peña-García, J.L. Abellán, H. Pérez-Sánchez, J. M. Cecilia, (2015) “Enhancing the parallelization of Non-Bonded Interactions Kernel for Virtual Screening on GPUs” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, 620-626.
  9. B. Imbernón, J. M. Cecilia, D. Giménez, (2015), “Enhancing Metaheuristic-based Virtual Screening Methods on Massively Parallel and Heterogeneous Systems”. Accepted for publication in International Workshop on Programming Models and Applications for Multicores and Manycores. ACM.

2014

Journals

  1. A. Pérez-Garrido, F. Girón-Rodríguez, A.M. Helguera, F. Borges, R.D. Combes, (2014), “Topological structural alerts modulations of mammalian cell mutagenicity for halogenated derivatives”. SAR and QSAR in Environmental Research, 25, pp. 17 – 33. ISSN 1062-936X
  2. I. Merelli, H. Pérez-Sánchez, S. Gesing, D. D’Agostino, (2014) “High-Performance Computing and Big Data in Omics-Based Medicine”, Biomed Research International, Article ID 825649.
  3. I. Merelli, D. D’Agostino, H. Pérez-Sánchez, S. Gesing, (2014) “Managing, Analysing and Integrating Big Data in medical bioinformatics: open problems and future perspectives”, Biomed Research International, DOI:10.1155/2014/134023.
  4. J.M. García-Martínez, E.M. Garzón, J.M. Cecilia, H. Pérez-Sánchez, P.M. Ortigosa, (2014) “An efficient approach for solving the HP Protein Folding Problem based on UEGO”, Journal of Mathematical Chemistry, (in press).
  5. G. Budryn, B. Palecz, D. Rachwal-Rosiak, J. Oracz, D. Zaczynska, S. Belica, I. Navarro-González, J. Vegara-Meseguer, H. Pérez-Sánchez, (2014), “Effect of inclusion of hydroxycinnamic and chlorogenic acids from green coffee bean in β-cyclodextrin on their interactions with whey, egg white and soy protein isolates ”, Food Chemistry (in press).
  6. J.P. Cerón-Carrasco, J. Cerezo, A. Requena, J. Zúñiga, J. Contreras-García, S. Chavan, M. Manrubia-Cobo, H. Pérez-Sánchez, (2014), “Labelling Herceptin with a novel oxaliplatin derivative: A computational approach towards the selective drug delivery”, Journal of Molecular Modeling, (in press).
  7. H. Pérez-Sánchez, G. Cano, J. García-Rodríguez, (2014), “Descubrimiento de Fármacos basado en Cribado Virtual Refinado con Enfoques Neuronales Paralelos”, Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería, (in press).
  8. Q. Bai, H. Pérez-Sánchez, Y. Zhang, Y. Shao, D. Shi, H. Liu, X. Yao, (2014) “Ligand Induced Change of β2 Adrenergic Receptor from Active to Inactive Conformation and Its Implication with Close and Open of Water Channel: Insight from Molecular Dynamics Simulation, Free Energy Calculation and Markov State Model Analysis”, Physical Chemistry Chemical Physics, (in press).
  9. G.D. Guerrero, B. Imbernón, H. Pérez-Sánchez, F. Sanz, J.M. García, J.M. Cecilia, (2014) “A Performance/Cost Evaluation for a GPU-Based Drug Discovery Application on Volunteer Computing”, BioMed Research International, (in press).
  10. I. Navarro-González, H. Pérez-Sánchez, G. Martin-Pozuelo, J. García-Alonso, M.J. Periago, (2013) “The inhibitor effects of bioactive compounds of tomato juice binding to hepatic HMGCR: in vivo study and molecular modelling”. PLOS ONE, DOI: 10.1371/journal.pone.0083968.
  11. V. Rezaei, H. Pezeshk, H. Pérez-Sánchez, (2013) “Generalized Baum-Welch Algorithm Based on The Similarity Between Sequences”, PLOS ONE, DOI: 10.1371/journal.pone.0080565.
  12. G. Cano, J. García, H. Pérez-Sánchez, (2014) “Improvement of Virtual Screening predictions using Computational Intelligence methods”, Letters in Drug Design & Discovery, 11(1), 33-39.
  13. H. Pérez-Sánchez, J.M. Cecilia, B. Imbernón Tudela, A. Pérez-Garrido, J. Soto, I. Timón-Pérez, J. García-Rodríguez, G. Cano, A. Bueno-Crespo, J. Vegara-Meseguer, (2014) “The Need for an Integrated Computational/Experimental Approach in the Discovery and Design of New Drugs”, Drug Designing, 3, e121, doi:10.4172/2169-0138.1000e121.

Conference proceedings

  1. J. Fang, A. Lucia Varbanescu, B. Imbernón, J. M. Cecilia, H. Peréz-Sánchez, (2014) “Parallel Computation of Non-Bonded Interactions in Drug Discovery: Nvidia GPUs vs. Intel Xeon Phi” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2014 (accepted).
  2. J. P. Cerón-Carrasco, J. Cerezo, J. Zúñiga, A. Requena, J. Contreras-García, S. Chavan, M. Manrubia-Cobo, B. Imbernón, J. M. Cecilia, H. Pérez-Sánchez, (2014) “Application of parallel blind docking with BINDSURF for the study of platinum derived compounds as anticancer drugs” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2014 (accepted).
  3. D. Bonetti, H. Pérez-Sánchez, A. Delbem, (2014) “An Efficient Solvent Accessible Surface Area calculation applied in Ab Initio Protein Structure Prediction” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2014 (accepted).
  4. D. Man, I. Timón-Pérez, J. Soto, A. Flores-Sintas, J. M. Cecilia, H. Pérez-Sánchez, (2014) “An improved Fuzzy Clustering methodology applied to the study of Protein Conformational Ensembles” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2014 (accepted).

2013

Journals

  1. J.M. López-Nicolas, M. Escorial-Camps, H. Pérez-Sánchez, F. García-Carmona, (2013) “Physicochemical and thermodynamic characterization of the encapsulation of methyl jasmonate by natural and modified cyclodextrins using reserved phase high pressure liquid chromatography”. Journal of Agriculural and Food Chemistry,  61(47), 11347-11354.
  2. H. Pérez-Sánchez, G. Cano, J. García, (2013) “Improving Drug Discovery using Hybrid Softcomputing Methods”. Applied Soft Computing, http://dx.doi.org/10.1016/j.asoc.2013.10.033.
  3. G.D. Guerreo, J.M. Cebrián, H. Pérez-Sánchez, J.M. García, M. Ujaldón, J.M. Cecilia, (2013) “Towards an energy efficient heterogenous processors: Findings on Virtual Screening methods”, Concurrency and Computation: Practice and Experience, doi: 10.1002/cpe.3119.
  4. G.D. Guerrero, R.M. Wallace, J.L. Vazquez-Poletti, J.M. Cecilia, J.M. García, D. Mozos, H. Pérez-Sánchez, (2013) “A Performance/Cost Model for a CUDA Drug Discovery Application on Physical and Public Cloud Infrastructures”, Concurrency and Computation: Practice and Experience, doi: 10.1002/cpe.3117.
  5. Q. Zhang, G.D. Guerrero, J.M. Cecilia, J.M. García, J. Wang, H. Pérez-Sánchez, T. Hou, (2013) “Accelerated Conformational Entropy Calculations using Graphic Processing Units”, Journal of Chemical Information and Modeling, 53, 2057-2064.
  6. I. Merelli, H. Pérez-Sánchez, S. Gesing, D. D’Agostino, (2013) “Latest Advances in Distributed, Parallel, and GPU-accelerated Approaches to Computational Biology”, Concurrency and Computation: Practice and Experience, doi: 10.1002/cpe.3111.
  7. H. Pérez-Sánchez, (2013) “Exploitation of Massively Parallel Architectures for Drug Discovery”, Drug Designing, 2, e108.
  8. Morales Helguera, Aliuska, Alfonso Pérez-Garrido, Alexandra Gaspar, Joana Reis, Fernando Cagide, Dolores Vina, M. Cordeiro, and Fernanda Borges. “Combining QSAR classification models for predictive modeling of human monoamine oxidase inhibitors.” European Journal of Medicinal Chemistry 59, (2013): 75-90.

Conference proceedings

  1. H. Pérez-Sánchez, G. D. Guerrero, J. M. Garcia, J. Peña, J. M. Cecilia, G. Cano, S. Orts-Escolano. J. Garcia-Rodriguez, (2012), “Improving Drug Discovery using a neural networks based parallel scoring function” In: International Joint Conference on Neural Networks, IJCNN 2013, 1436-1440..
  2. G. Cano, M. Manrubia-Cobo, H. den-Haan, J. García-Rodríguez, H. Pérez-Sánchez, (2013) “Improvement of Virtual Screening predictions using Support Vector Machines” In: 13th International Conference on Computational and Mathematical Methods in Science and Engineering (CMMSE 2013), (accepted).
  3. H. Pérez-Sánchez, G.D. Guerrero, F. Sanz, J.M. Cecilia, (2013) “A GPU based Volunteer Computing Platform for the discovery of bioactive compounds” In: 13th International Conference on Computational and Mathematical Methods in Science and Engineering (CMMSE 2013), (accepted).
  4. J. Peña, J. M. Cecilia, H. Pérez-Sánchez, (2013) “Application of Ant Colony Optimization in an hybrid coarse-grained and all-atom based Protein Structure prediction strategy” In: 13th International Conference on Computational and Mathematical Methods in Science and Engineering (CMMSE 2013), (accepted).
  5. G.D. Guerrero, J.M. Cecilia, J.M. García, H. Pérez-Sánchez, (2013) “Impact of implicit solvation models on database enrichment in GPU based blind Virtual Screening” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2013, 731-734.
  6. Q. Zhang, J.M. García, J. Wang, T. Hou, H. Pérez-Sánchez, (2013) “A GPU based Conformational Entropy Calculation Method” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2013, 735-744.

2012

Journals

  1. J. Navarro-Fernández, H. Pérez-Sánchez, I. Martínez-Martínez, I. Meliciani, J.A. Guerrero, V. Vicente, J. Corral, W. Wenzel, (2012) “In-silico discovery of a compound with nanomolar affinity to antithrombin causing partial activation and increased heparin affinity”, Journal of Medicinal Chemistry, 55(14), 6403-6412.
  2. I. Sánchez-Linares, H. Pérez-Sánchez, J.M. Cecilia, J.M. García, (2012) “High-Throughput parallel blind Virtual Screening using BINDSURF”, BMC Bioinformatics, 13(Suppl 14):S13 (Highly accessed).Irene Sánchez-Linares, Horacio Pérez-Sánchez, José M. Cecilia and José M. García. High-Throughput parallel blind Virtual Screening using BINDSURF. BMC Bioinformatics 2012, 13 (Suppl 14):S13 (7 September 2012).
  3. Ruiz, G.; De Vicente, E.; Vegara, J. (2012) “Sedentary behavior and physical activity levels in university students and workers”. Journal of Sport and Health research, 4(1): 83-92
  4. H. Pérez-Sánchez, E. J. Cepas Quiñonero, J.M. Cecilia, and J. M. García, (2012) “Parallel blind Virtual Screening with implicit solvation models” In: Applied Computing 2012 (IADIS), 421-423.
  5. Alfonso Pérez-Garrido, Alfonso, Aliuska Morales Helguera, Juana M. Morillas Ruiz, Pilar Zafrilla Rentero. “Topological sub-structural molecular design approach: Radical scavenging activity”. European Journal of Medicinal Chemistry 49, (2012): 86-94

Conference proceedings

  1. G.D. Guerrero, H. Pérez-Sánchez, J.M. Cecilia, J.M. García, (2012) “Parallelization of Virtual Screening in Drug Discovery on Massively Parallel Architectures” In: 20th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing PDP 2012, 588-595.
  2. E. J. Cepas Quiñonero, P. Koehl, H. Pérez-Sánchez, and J. M. García, (2012) “Analytical solvent accessible surface area calculation on GPUs” In: 12th International Conference on Computational and Mathematical Methods in Science and Engineering (CMMSE 2012), 307-309.

2011

Journals

  1. H. Pérez-Sánchez, W. Wenzel, (2011) “Optimization methods for virtual screening on novel computational architectures”, Current Computer Aided Drug Design, 7, 44-52.
  2. Pérez-Garrido, Alfonso, Aliuska Morales Helguera, Fernanda Borges, M. Natália DS Cordeiro, Virginia Rivero, and Amalio Garrido Escudero. “Two new parameters based on distances in a receiver operating characteristic chart for the selection of classification models.” Journal of Chemical Information and Modeling 51, no. 10 (2011): 2746-2759.

Conference proceedings

  1. G.D. Guerrero, H. Pérez-Sánchez, W. Wenzel, J.M. Cecilia, J.M. García, (2011) “Effective Non-Bonded Interactions Kernel for Virtual Screening on emergent parallel architectures”, In PACBB11, 5th International Conference on Practical Applications of Computational Biology & Bioinformatics. Advances in Intelligent and Soft Computing, 93, 63-69.
  2. I. Sánchez-Linares, H. Pérez-Sánchez, J.M. García, (2012) “Accelerating Grid Kernels for Virtual Screening on Graphics Processing Units” In: Proceedings of the 2011 International Conference on Parallel Computing (ParCo 2011), Advances in Parallel Computing (22), 413-420.
  3. H. Pérez-Sánchez, I. Kondov, J.M. García, K. Klenin, W. Wenzel, (2011) “A Pipeline Pilot based SOAP implementation of FlexScreen for High-Throughput Virtual Screening” In: IWSG-Life 2011 (3rd International Workshop on Science Gateways for Life Sciences).
  4. I. Sánchez-Linares, H. Pérez-Sánchez, G.D. Guerrero, J.M. Cecilia, J.M. García, (2011) “Accelerating multiple target drug screening on GPUs” In: CMSB 2011 (9th International Conference on Computational Methods in Systems Biology).
  5. I. Sánchez-Linares, H. Pérez-Sánchez, J.M. Cecilia, J.M. García, (2011) “BINDSURF: a fast blind Virtual Screening methodology on GPUs” In: NETTAB 2011 workshop focused on Clinical Bioinformatics, 95-97.
  6. E. J. Cepas Quiñonero, H. Pérez-Sánchez, J.M. Cecilia, J.M. García, (2011) “MURCIA: Fast parallel solvent accessible surface area calculation on GPUs and application to drug discovery and molecular visualization” In: NETTAB 2011 workshop focused on Clinical Bioinformatics, 52-55.

2010

Journals

  1. J. García de la Torre, F.G. Díaz Baños, H.E. Pérez Sánchez, (2010) “Kerr constant of multi-subunit particles and semiflexible, wormlike chains”, Journal of Physics : Condensed Matter, 22,
  2. Pérez-Garrido, Alfonso, Aliuska Morales Helguera, Gabriel Caravaca López, M.Natália D.S. Cordeiro, and Amalio Garrido Escudero. “A topological substructural molecular design approach for predicting mutagenesis end-points of α, β-unsaturated carbonyl compounds”. Toxicology 268, no 1-2 (2010): 64–77.
  3. Pérez-Garrido, Alfonso, Aliuska Morales Helguera, Francisco Girón Rodríguez, and M. N. D. S. Cordeiro. “QSAR models to predict mutagenicity of acrylates, methacrylates and, α, β-unsaturated carbonyl compounds.” Dental Materials 26, no. 5 (2010): 397-415.

2009

Journals

  1. J. García de la Torre, J.G. Hernández Cifre, A. Ortega, R. Rodríguez Schmidt, M.X. Fernandes, H.E. Pérez Sánchez, R. Pamies, (2009) “SIMUFLEX: Algorithms and tools for simulation of the conformation and dynamics of flexible molecules and nanoparticles in dilute solution”. Journal of Chemical Theory and Computation, 5, 2606-2618.

Conference proceedings

  1. H.E. Pérez Sánchez and W. Wenzel. “Implementation of an effective non-bonded interactions kernel for biomolecular simulations on the Cell processor”. In Proceedings of Massively Parallel Computational Biology on GPUs, Jahrestagung der Gesellschaft für Informatik e.V., Lübeck, Germany, September 29, 2009. Volume 154 of Lecture Notes in Informatics, 721-729.

2008

Journals

  1. Pérez-Garrido, Alfonso, Maykel Pérez-González, and Amalio Garrido Escudero. “Halogenated derivatives QSAR model using spectral moments to predict haloacetic acids (HAA) mutagenicity”. Bioorganic & Medicinal Chemistry 16, no. 10 (2008): 5720–5732.

Conference proceedings

  1. “High Throughput in-silico Screening against flexible protein receptors”, H.E. Pérez Sánchez, B. Fischer, H. Merlitz and W. Wenzel. NIC Workshop 2008, From Computational Biophysics to Systems Biology, Jan Meinke, Ulrich H.E. Hansmann (Editors) John von Neumann Institute for Computing, Jülich, NIC Series, 40, 133-136.

2006

Journals

  1. H.E. Pérez Sánchez, K. Tatarenko, M. Nigen, A. Imberty, Hs. Lortat-Jacob, J. García de la Torre, C. Ebel, (2006) “Organization of human interferon gamma heparin complexes from solution properties and hydrodynamics”. Biochemistry, 45, 13227-13238.
  2. *P. Vaca, *F. Martín, J.M. Vegara-Meseguer, J.M. Rovira, G. Berná, B. Soria (2006) “Induction of differentiation of ES cells into islet cells by Fetal Soluble Factors”. Stem Cells, 24: 258-265.

2005

Journals

  1. J. García de la Torre, A. Ortega, H.E. Pérez Sánchez, J.G. Hernandez Cifre, (2005) “MULTYHYDRO and MONTEHYDRO: Conformational search and Monte Carlo calculation of solution properties of rigid or flexible bead models”. Biophysical Chemistry, 116, 121-128.
  2. H.E. Pérez Sánchez, J. García de la Torre, F.G. Díaz Baños, (2005) “Transient electric birefringence of wormlike macromolecules in electric fields of arbitrary strength: A computer simulation study”. Journal of Chemical Physics, 122, 124902-1, 12.
  3. J.M. Vegara-Meseguer, B. Soria, (2005) “Ion channels in the plasma membrane of mouse embryonic stem cells and their physiological role”. Journal of Physiology and Biochemistry, 61, 1.
  4. Andrés Bueno-Crespo, José Luis Sancho-Gómez, Rafaél Verdú, (2005) “Artificial Construction of Task for Multitask Learning.”, IADAT JOURNAL of Advanced Technology on Imaging and Graphics; 1, 50-52. ISSN: 1885-6411

2003

Journals

  1. H.E. Pérez Sánchez, J. García de la Torre, F.G. Díaz Baños, (2003) “Birefringence, deformation and scattering of wormlike macromolecules under an external agent. Steady-state properties in an electric field”. Journal of Physical Chemistry, B. , 107, 13192-13200.
  2. J. García de la Torre, H.E. Pérez Sánchez, A. Ortega, J.G. Hernández, M.X. Fernandes, F.G. Díaz, M.C. López Martínez, (2003) “Calculation of the solution properties of flexible macromolecules: methods and application”. European Biophysics Journal, 32, 477-486.

2002

Journals

  1. H.E. Pérez Sánchez, J. García de la Torre, F.G. Díaz Baños, (2002) “Influence of field strength and flexibility on the transient electric birefringence of segmentally flexible macromolecules”. Journal of Physical Chemistry, B., 106, 6754-6761.
  2. B. Soria, T. León-Quinto, J. Jones, P. Sepulcre, J.M. Vegara-Meseguer, P. Vaca, G. Berná, E. Roche, J.A. Reig, F. Martín, (2002) “Estrategias para la obtención de células productoras de insulina a partir de células madre”, Fundación Valenciana de Estudios Avanzados. Generalitat Valenciana. Conselleria de Sanitat.
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