Abstract
Nature as a source of inspiration has been shown to have a great beneficial impact on the development of new computational methodologies. In this scenario, analyses of the interactions between a protein target and a ligand can be simulated by biologically inspired algorithms (BIAs). These algorithms mimic biological systems to create new paradigms for computation, such as neural networks, evolutionary computing, and swarm intelligence. This review provides a description of the main concepts behind BIAs applied to molecular docking simulations. Special attention is devoted to evolutionary algorithms, guided-directed evolutionary algorithms, and Lamarckian genetic algorithms. Recent applications of these methodologies to protein targets identified in the Mycobacterium tuberculosis genome are described.
Keywords: Bio-inspired computing, evolutionary algorithms, molecular docking, structure-based virtual screening, protein-ligand, docking, InhA, PNP, EPSP synthase, quantum states
Current Medicinal Chemistry
Title: Bio-Inspired Algorithms Applied to Molecular Docking Simulations
Volume: 18 Issue: 9
Author(s): G. Heberle and W. F. de Azevedo
Affiliation:
Keywords: Bio-inspired computing, evolutionary algorithms, molecular docking, structure-based virtual screening, protein-ligand, docking, InhA, PNP, EPSP synthase, quantum states
Abstract: Nature as a source of inspiration has been shown to have a great beneficial impact on the development of new computational methodologies. In this scenario, analyses of the interactions between a protein target and a ligand can be simulated by biologically inspired algorithms (BIAs). These algorithms mimic biological systems to create new paradigms for computation, such as neural networks, evolutionary computing, and swarm intelligence. This review provides a description of the main concepts behind BIAs applied to molecular docking simulations. Special attention is devoted to evolutionary algorithms, guided-directed evolutionary algorithms, and Lamarckian genetic algorithms. Recent applications of these methodologies to protein targets identified in the Mycobacterium tuberculosis genome are described.
Export Options
About this article
Cite this article as:
Heberle G. and F. de Azevedo W., Bio-Inspired Algorithms Applied to Molecular Docking Simulations, Current Medicinal Chemistry 2011; 18 (9) . https://dx.doi.org/10.2174/092986711795029573
DOI https://dx.doi.org/10.2174/092986711795029573 |
Print ISSN 0929-8673 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-533X |
Call for Papers in Thematic Issues
Advances in Medicinal Chemistry: From Cancer to Chronic Diseases.
The broad spectrum of the issue will provide a comprehensive overview of emerging trends, novel therapeutic interventions, and translational insights that impact modern medicine. The primary focus will be diseases of global concern, including cancer, chronic pain, metabolic disorders, and autoimmune conditions, providing a broad overview of the advancements in ...read more
Approaches to the treatment of chronic inflammation
Chronic inflammation is a hallmark of numerous diseases, significantly impacting global health. Although chronic inflammation is a hot topic, not much has been written about approaches to its treatment. This thematic issue aims to showcase the latest advancements in chronic inflammation treatment and foster discussion on future directions in this ...read more
Cellular and Molecular Mechanisms of Non-Infectious Inflammatory Diseases: Focus on Clinical Implications
The Special Issue covers the results of the studies on cellular and molecular mechanisms of non-infectious inflammatory diseases, in particular, autoimmune rheumatic diseases, atherosclerotic cardiovascular disease and other age-related disorders such as type II diabetes, cancer, neurodegenerative disorders, etc. Review and research articles as well as methodology papers that summarize ...read more
Chalcogen-modified nucleic acid analogues
Chalcogen-modified nucleosides, nucleotides and oligonucleotides have been of great interest to scientific research for many years. The replacement of oxygen in the nucleobase, sugar or phosphate backbone by chalcogen atoms (sulfur, selenium, tellurium) gives these biomolecules unique properties resulting from their altered physical and chemical properties. The continuing interest in ...read more
- Author Guidelines
- Graphical Abstracts
- Fabricating and Stating False Information
- Research Misconduct
- Post Publication Discussions and Corrections
- Publishing Ethics and Rectitude
- Increase Visibility of Your Article
- Archiving Policies
- Peer Review Workflow
- Order Your Article Before Print
- Promote Your Article
- Manuscript Transfer Facility
- Editorial Policies
- Allegations from Whistleblowers
- Announcements
Related Articles
-
Potential of Nanocarriers in Genetic Immunization
Recent Patents on Drug Delivery & Formulation Current Developments of Coumarin Compounds in Medicinal Chemistry
Current Pharmaceutical Design Metal-N-Heterocyclic Carbene Complexes as Anti-Tumor Agents
Current Medicinal Chemistry Effect of Contrast-enhanced Contemporaneous <sup>18</sup>F-FDG PET/CT on Semi Quantification Uptake Value Using Third Party Viewing Workstation
Recent Patents on Medical Imaging Modern Therapeutic Strategies for Autoimmune Diseases
Current Pharmaceutical Design Circumscribing the Conformational Peptide Epitope Landscape
Current Pharmaceutical Design Multifocal Osteolytic Lesions in Skull Bone with Mycobacterium <i>Tuberculosis</i>: A Case Report
Infectious Disorders - Drug Targets Lyn Regulates Cytotoxicity in Respiratory Epithelial Cells Challenged by Cigarette Smoke Extracts
Current Molecular Medicine A Novel Advanced Laboratory Diagnosis to Guide Tuberculosis Drug Therapy.
Recent Patents on Anti-Infective Drug Discovery HIV Nef: Role in Pathogenesis and Viral Fitness
Current HIV Research Adaptors in Toll-Like Receptor Signaling and their Potential as Therapeutic Targets
Current Drug Targets Recent Advances in Nanoparticle Carriers for Coordination Complexes
Current Topics in Medicinal Chemistry Isolation, Biological Activities and Synthesis of Indoloquinoline Alkaloids: Cryptolepine, Isocryptolepine and Neocryptolepine
Current Organic Chemistry Novel Inhibitors of Inosine Monophosphate Dehydrogenase in Patent Literature of the Last Decade
Recent Patents on Anti-Cancer Drug Discovery MiR-147: Functions and Implications in Inflammation and Diseases
MicroRNA The Relative Transcription Index: A Gene Expression Based Metric for Prioritization of Drug Candidates
Combinatorial Chemistry & High Throughput Screening Controlled Delivery of Biotechnological Products
Current Pharmaceutical Biotechnology Design and Synthesis of Novel Oxadiazole and Diphenyl Ether Hydrazone Derivatives of Coumarin as Potential Antibacterial Agents
Current Bioactive Compounds Patent Selections
Recent Patents on Biotechnology The Central Role Played by Peptides in the Immune Response and the Design of Peptide-Based Vaccines Against Infectious Diseases and Cancer
Current Drug Targets