Abstract
In this review, several aspects of virtual screening are presented. Although, docking and scoring have been the most widely employed techniques, ligand-based virtual screening has also gained momentum in recent years. We have classified the docking programs into four categories, based on their underline theories, and accordingly describe the most up-to-date algorithms and newest versions. Similarly, three categories of scoring functions are presented, while their weighting schemes on particular binding terms are discussed. The latter is important, since knowledge of the function can be used to select the ones that could be more appropriate for targets of similar nature. Challenging aspects, such as protein flexibility and practices to select the most appropriate docking/scoring schemes, are also discussed. Finally, a real-life example is presented where a pharmacophore-driven approach combined with a docking exercise were undertaken in an iterative manner to successfully enhance the virtual screening hit rates. In the end, we present our own perspective for best practices in the field based on our experiences.
Keywords: Drug discovery, virtual screening, docking, scoring
Current Medicinal Chemistry
Title: Theoretical and Practical Considerations in Virtual Screening: A Beaten Field?
Volume: 15 Issue: 2
Author(s): Maria Kontoyianni, Prakash Madhav, Eric Suchanek and William Seibel
Affiliation:
Keywords: Drug discovery, virtual screening, docking, scoring
Abstract: In this review, several aspects of virtual screening are presented. Although, docking and scoring have been the most widely employed techniques, ligand-based virtual screening has also gained momentum in recent years. We have classified the docking programs into four categories, based on their underline theories, and accordingly describe the most up-to-date algorithms and newest versions. Similarly, three categories of scoring functions are presented, while their weighting schemes on particular binding terms are discussed. The latter is important, since knowledge of the function can be used to select the ones that could be more appropriate for targets of similar nature. Challenging aspects, such as protein flexibility and practices to select the most appropriate docking/scoring schemes, are also discussed. Finally, a real-life example is presented where a pharmacophore-driven approach combined with a docking exercise were undertaken in an iterative manner to successfully enhance the virtual screening hit rates. In the end, we present our own perspective for best practices in the field based on our experiences.
Export Options
About this article
Cite this article as:
Kontoyianni Maria, Madhav Prakash, Suchanek Eric and Seibel William, Theoretical and Practical Considerations in Virtual Screening: A Beaten Field?, Current Medicinal Chemistry 2008; 15 (2) . https://dx.doi.org/10.2174/092986708783330566
DOI https://dx.doi.org/10.2174/092986708783330566 |
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
-
Effects of Physical Exercise on Inflammatory Markers of Atherosclerosis
Current Pharmaceutical Design Impact of Pressure Drop on Pulse Wave Velocity Along Experimental Stenoses
Vascular Disease Prevention (Discontinued) Mitochondrial Aldehyde Dehydrogenase, A Potential Drug Target for Protection of Heart and Brain from Ischemia/Reperfusion Injury
Current Drug Targets Editorial (Thematic Issue: The Crosstalk between Non-Pharmaceutical and Pharmaceutical Approaches to Prevention and Treatment of Chronic Diseases: Current Concepts and Perspectives)
Current Pharmaceutical Design Dyslipidaemia, Hypercoagulability and the Metabolic Syndrome
Current Vascular Pharmacology Intrauterine Effects of Impaired Lipid Homeostasis in Pregnancy Diseases
Current Medicinal Chemistry Brachial-Ankle Pulse Wave Velocity as a Novel Measure of Arterial Stiffness: Present Evidences and Perspectives
Current Hypertension Reviews Prognostic Value of Copeptin in Chronic Kidney Disease: From General Population to End-Stage Renal Disease
Current Protein & Peptide Science Genetics and Genomics of Hepatic Acute Phase Reactants: A Mini-Review
Inflammation & Allergy - Drug Targets (Discontinued) Compared Chemical Activity and Effects on Cell Viability of Various Antioxidant Compounds
Current Analytical Chemistry Psoriasis and Vascular Risk : An Update
Current Pharmaceutical Design Hypertension, Prehypertension and Blood Pressure Related Diseases
Immunology, Endocrine & Metabolic Agents in Medicinal Chemistry (Discontinued) Pregnancy Complicated by the Most Frequent Forms of Maturity Onset Diabetes of the Young: A Narrative Review on Its Pharmacological Implications
Current Reviews in Clinical and Experimental Pharmacology Editorial (Hot Topic: Achieving Current Goals in Prevention and Treatment of Vascular Disease: An Update)
Current Pharmaceutical Design Lipoprotein Subfractions, Uric Acid and Cardiovascular Risk in End-Stage Renal Disease (ESRD) Patients
Current Vascular Pharmacology Preventive and Therapeutic Potentials of Anthocyanins in Diabetes and Associated Complications
Current Medicinal Chemistry Vildagliptin Restores Renal Myogenic Function and Attenuates Renal Sclerosis Independently of Effects on Blood Glucose or Proteinuria in Zucker Diabetic Fatty Rat
Current Vascular Pharmacology ABC Transporters and Sterol Absorption
Current Drug Targets - Cardiovascular & Hematological Disorders Obesity and Inflammation and Altered Clopidogrel Pharmacokinetics and Pharmacodynamics
Drug Metabolism Letters Diabetes and Complications: Cellular Signaling Pathways, Current Understanding and Targeted Therapies
Current Drug Targets