![]() In BINDSURF ( Sánchez-Linares et al., 2012), the protein surface is divided into independent regions (or spots), and GPUs are used to perform simultaneous docking simulations for each ligand at all the spots. Docking simulations are typically carried out at the protein surface using well-known methods, like Autodock ( Morris et al., 1998), Glide ( Friesner et al., 2004), DOCK ( Ewing et al., 2001), FMD ( Dolezal et al., 2015), or BUDE ( McIntosh-Smith et al., 2015). The computation of the potential is usually the most time-consuming calculation, taking up to 80% of the total execution time ( Kuntz et al., 2001). They look for the optimal binding sites ranking chemical compounds according to the estimated scoring function ( Schneider, 2002). Molecular Docking techniques for VS simulate the docking process of small molecules in the structures of macromolecular targets. On the other hand, the repeated application of metaheuristics means large execution times, which requires parallelism in the search for satisfactory metaheuristics. On the one hand, the parameterized schema facilitates the application and tuning of several metaheuristics just by varying the values of the metaheuristic parameters, so some methods for selecting the parameters should be implemented. The use of METADOCK brings with it two main problems. Massive parallelism and heterogeneous architectures are exploited, including multicore central processing units (CPUs), graphics processing units (GPUs), nodes of CPU + multi-GPU, and clusters with nodes of this type. Scoring functions are computed for different conformations of the ligand at several binding spots throughout the receptor surface. (2018b) and uses a parameterized schema of metaheuristics to generate a wide range of metaheuristics, with each one corresponding to a set of values for some metaheuristic parameters. METADOCK is a software for molecular docking to predict non-covalent binding between a receptor and a ligand. The efficient exploitation of these systems enables HYPERDOCK to improve ligand–receptor binding. The different levels of parallelism can be used to exploit the parallelism offered by computational systems composed of multicore CPU + multi-GPUs. HYPERDOCK exploits the parallelism of METADOCK and includes parallelism at its own level. Multiple metaheuristics are explored, so the process is computationally demanding. HYPERDOCK represents a step forward the exploration for satisfactory metaheuristics is systematically approached by means of hyperheuristics working on top of the metaheuristic schema of METADOCK. METADOCK is a tool for the application of metaheuristics to VS in heterogeneous clusters of computers based on central processing unit (CPU) and graphics processing unit (GPU). The computational requirements of VS, along with the size of the databases, propitiate the use of high-performance computing. Virtual screening (VS) methods aid clinical research by predicting the interaction of ligands with pharmacological targets. ![]() ![]() ![]() All subjects Allied Health Cardiology & Cardiovascular Medicine Dentistry Emergency Medicine & Critical Care Endocrinology & Metabolism Environmental Science General Medicine Geriatrics Infectious Diseases Medico-legal Neurology Nursing Nutrition Obstetrics & Gynecology Oncology Orthopaedics & Sports Medicine Otolaryngology Palliative Medicine & Chronic Care Pediatrics Pharmacology & Toxicology Psychiatry & Psychology Public Health Pulmonary & Respiratory Medicine Radiology Research Methods & Evaluation Rheumatology Surgery Tropical Medicine Veterinary Medicine Cell Biology Clinical Biochemistry Environmental Science Life Sciences Neuroscience Pharmacology & Toxicology Biomedical Engineering Engineering & Computing Environmental Engineering Materials Science Anthropology & Archaeology Communication & Media Studies Criminology & Criminal Justice Cultural Studies Economics & Development Education Environmental Studies Ethnic Studies Family Studies Gender Studies Geography Gerontology & Aging Group Studies History Information Science Interpersonal Violence Language & Linguistics Law Management & Organization Studies Marketing & Hospitality Music Peace Studies & Conflict Resolution Philosophy Politics & International Relations Psychoanalysis Psychology & Counseling Public Administration Regional Studies Religion Research Methods & Evaluation Science & Society Studies Social Work & Social Policy Sociology Special Education Urban Studies & Planning BROWSE JOURNALS ![]()
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