Abstract
Driven by a steady improvement of computational hardware and significant progress in ab initio method development, quantum-mechanical approaches can now be applied to large biochemical systems and drug design. We review the methods implemented in GAMESS, which are suitable to calculate large biochemical systems. An emphasis is put on the fragment molecular orbital method (FMO) and quantum mechanics interfaced with molecular mechanics (QM/MM). The use of FMO in the protein-ligand binding, structure-activity relationship (SAR) studies, fragment- and structure-based drug design (FBDD/SBDD) is discussed in detail.
Keywords: Quantum chemistry, fragment molecular orbital, drug design, ab initio, GAMESS, FMO, QM/MM, FBDD, SBDD.
Current Topics in Medicinal Chemistry
Title:GAMESS As a Free Quantum-Mechanical Platform for Drug Research
Volume: 12 Issue: 18
Author(s): Yuri Alexeev, Michael P. Mazanetz, Osamu Ichihara and Dmitri G. Fedorov
Affiliation:
Keywords: Quantum chemistry, fragment molecular orbital, drug design, ab initio, GAMESS, FMO, QM/MM, FBDD, SBDD.
Abstract: Driven by a steady improvement of computational hardware and significant progress in ab initio method development, quantum-mechanical approaches can now be applied to large biochemical systems and drug design. We review the methods implemented in GAMESS, which are suitable to calculate large biochemical systems. An emphasis is put on the fragment molecular orbital method (FMO) and quantum mechanics interfaced with molecular mechanics (QM/MM). The use of FMO in the protein-ligand binding, structure-activity relationship (SAR) studies, fragment- and structure-based drug design (FBDD/SBDD) is discussed in detail.
Export Options
About this article
Cite this article as:
Alexeev Yuri, P. Mazanetz Michael, Ichihara Osamu and G. Fedorov Dmitri, GAMESS As a Free Quantum-Mechanical Platform for Drug Research, Current Topics in Medicinal Chemistry 2012; 12 (18) . https://dx.doi.org/10.2174/1568026611212180008
DOI https://dx.doi.org/10.2174/1568026611212180008 |
Print ISSN 1568-0266 |
Publisher Name Bentham Science Publisher |
Online ISSN 1873-4294 |
Call for Papers in Thematic Issues
Chemistry Based on Natural Products for Therapeutic Purposes
The development of new pharmaceuticals for a wide range of medical conditions has long relied on the identification of promising natural products (NPs). There are over sixty percent of cancer, infectious illness, and CNS disease medications that include an NP pharmacophore, according to the Food and Drug Administration. Since NP ...read more
Current Trends in Drug Discovery Based on Artificial Intelligence and Computer-Aided Drug Design
Drug development discovery has faced several challenges over the years. In fact, the evolution of classical approaches to modern methods using computational methods, or Computer-Aided Drug Design (CADD), has shown promising and essential results in any drug discovery campaign. Among these methods, molecular docking is one of the most notable ...read more
Drug Discovery in the Age of Artificial Intelligence
In the age of artificial intelligence (AI), we have witnessed a significant boom in AI techniques for drug discovery. AI techniques are increasingly integrated and accelerating the drug discovery process. These developments have not only attracted the attention of academia and industry but also raised important questions regarding the selection ...read more
From Biodiversity to Chemical Diversity: Focus of Flavonoids
Flavonoids are the largest group of polyphenols, plant secondary metabolites arising from the essential aromatic amino acid phenylalanine (or more rarely from tyrosine) via the phenylpropanoid pathway. The flavan nucleus is the basic 15-carbon skeleton of flavonoids (C6-C3-C6), which consists of two phenyl rings (A and B) and a heterocyclic ...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
-
Adiposity and Alzheimers Disease
Current Alzheimer Research Phytometabolites Targeting the Warburg Effect in Cancer Cells: A Mechanistic Review
Current Drug Targets Functional RNAs as Tools in Proteomics
Current Proteomics Adult Stem Cells for Cartilage Tissue Engineering and Regeneration
Current Rheumatology Reviews Inhibition of Intercellular Communication between Prostate Cancer Cells by A Specific Anti-STEAP-1 Single Chain Antibody
Anti-Cancer Agents in Medicinal Chemistry Preface
Current Pharmaceutical Design Recent Patents on Liposomal-Based Chemotherapeutics with a Triggered Release Mechanism
Recent Patents on Nanomedicine Patent Selections
Recent Patents on Anti-Infective Drug Discovery A Review on Aptamers Selection and Application in Heart Diseases Diagnosis
Current Topics in Medicinal Chemistry Some Important Dietary Polyphenolic Compounds: An Anti-inflammatory and Immunoregulatory Perspective
Mini-Reviews in Medicinal Chemistry Overview on Plant Antimicrobial Peptides
Current Protein & Peptide Science Musculoskeletal Adverse Drug Reactions: A Review of Literature and Data from ADR Spontaneous Reporting Databases
Current Drug Safety An Overview of Immune Evasion Strategies of DNA and RNA Viruses
Infectious Disorders - Drug Targets The Anterior Gradient-2 Pathway as a Model for Developing Peptide-Aptamer Anti-Cancer Drug Leads that Stimulate p53 Function
Current Chemical Biology Does Osteoblast to Adipocyte Differentiation Play a Role in Osteoarthritis?
Current Rheumatology Reviews Effect of Simultaneous Snail Slime-aided Degradation and Yeast Fermentation on Terpenoid Composition of Plantain Pseudostem Waste
Current Pharmaceutical Biotechnology Successful Applications of Computer Aided Drug Discovery: Moving Drugs from Concept to the Clinic
Current Topics in Medicinal Chemistry Anti-Allergic Potential of Herbs and Herbal Natural Products - Activities and Patents
Recent Patents on Endocrine, Metabolic & Immune Drug Discovery Exploring the Management of Statin Intolerant Patients: 2016 and Beyond
Current Vascular Pharmacology HIV Infection and Myocardial Infarction
Current HIV Research