Abstract
Carbohydrates are often referred to as the third molecular chain of life, and they represent the most important post-genomics research targets. Recent reports of their biological functions in signal transduction and cellular recognition have made them promising pharmaceutical targets and disease markers. Like nucleic acids and proteins, the three-dimensional (3D) structures of carbohydrates are important for their molecular functions. Currently, the most abundant source of biological carbohydrate structures is the Protein Data Bank (PDB). As its name indicates, the PDB is a protein structure database. However, carbohydrate structures have often been determined in complexes with protein molecules, as enzyme substrates, lectin ligands, or post-translational modifications. As of Jul 2006, the PDB contained 6,421 carbohydrate-protein complex structures, and the number is increasing rapidly. In this review, the current status of the PDB as the carbohydrate structure database, and the features of several databases derived from the PDB will be summarized. We will also introduce an overview of the bioinformatics tools currently available for analyses of carbohydrate 3D structures.
Keywords: hidden Markov models, Structural genomics, N-glycans, getCARBO program, Glycoconjugate Data Bank
Current Chemical Biology
Title: Current Aspects of Carbohydrate Structural Bioinformatics
Volume: 1 Issue: 3
Author(s): Taku Nakahara, Shin-Ichiro Nishimura and Tsuyoshi Shirai
Affiliation:
Keywords: hidden Markov models, Structural genomics, N-glycans, getCARBO program, Glycoconjugate Data Bank
Abstract: Carbohydrates are often referred to as the third molecular chain of life, and they represent the most important post-genomics research targets. Recent reports of their biological functions in signal transduction and cellular recognition have made them promising pharmaceutical targets and disease markers. Like nucleic acids and proteins, the three-dimensional (3D) structures of carbohydrates are important for their molecular functions. Currently, the most abundant source of biological carbohydrate structures is the Protein Data Bank (PDB). As its name indicates, the PDB is a protein structure database. However, carbohydrate structures have often been determined in complexes with protein molecules, as enzyme substrates, lectin ligands, or post-translational modifications. As of Jul 2006, the PDB contained 6,421 carbohydrate-protein complex structures, and the number is increasing rapidly. In this review, the current status of the PDB as the carbohydrate structure database, and the features of several databases derived from the PDB will be summarized. We will also introduce an overview of the bioinformatics tools currently available for analyses of carbohydrate 3D structures.
Export Options
About this article
Cite this article as:
Nakahara Taku, Nishimura Shin-Ichiro and Shirai Tsuyoshi, Current Aspects of Carbohydrate Structural Bioinformatics, Current Chemical Biology 2007; 1 (3) . https://dx.doi.org/10.2174/2212796810701030265
DOI https://dx.doi.org/10.2174/2212796810701030265 |
Print ISSN 2212-7968 |
Publisher Name Bentham Science Publisher |
Online ISSN 1872-3136 |
- 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
-
Understanding Stem Cell-Mediated Brain Repair Through Neuroimaging
Current Stem Cell Research & Therapy Protein Oxidative Modification in the Aging Organism and the Role of the Ubiquitin Proteasomal System
Current Pharmaceutical Design Wolbachia and Its Implications for the Immunopathology of Filariasis
Endocrine, Metabolic & Immune Disorders - Drug Targets Pharmacotherapy & Surgical Interventions Available for Obesity Management and Importance of Pancreatic Lipase Inhibitory Phytomolecules as Safer Anti-Obesity Therapeutics
Mini-Reviews in Medicinal Chemistry Dietary Interventions in Asthma
Current Pharmaceutical Design Ionotropic Glutamate Receptors & CNS Disorders
CNS & Neurological Disorders - Drug Targets Coated with Nanomaterials Intraocular Lenses, Ophthalmic and Human Body Implantable Devices with High Catalytic Antioxidant Activities: A New Nanotechnology Strategy of Peroxidase Cellular Enzyme Mimics Increasing the Biocompatibility and Therapeutic Deployment of the Medical Prosthetic Device
Recent Patents on Drug Delivery & Formulation Modulation of Cell Death in Age-Related Diseases
Current Pharmaceutical Design Cognitive Impairment and Dementia in Patients with Parkinson Disease
Current Topics in Medicinal Chemistry Pituitary Adenylate Cyclase Activating Polypeptide: A Potential Neuroprotective Peptide
Current Pharmaceutical Design Altered Biological Rhythm and Alzheimer's Disease: A Bidirectional Relationship
Current Alzheimer Research Ghrelin and Motilin in the Gastrointestinal System
Current Pharmaceutical Design The Alzheimer Pandemic: Is Paracetamol to Blame?
Inflammation & Allergy - Drug Targets (Discontinued) NF-κB Signature on the Aging Wall
Current Drug Metabolism Therapeutic Perspectives of Drugs Targeting Toll-Like Receptors Based on Immune Physiopathology Theory of Alzheimers Disease
CNS & Neurological Disorders - Drug Targets Mild Parkinsonian Signs in a Hospital-based Cohort of Mild Cognitive Impairment Types: A Cross-sectional Study
Current Alzheimer Research Microparticles: From Biogenesis to Biomarkers and Diagnostic Tools in Cardiovascular Disease
Current Stem Cell Research & Therapy Molecular Mechanisms Triggered by Bile Acids on Intestinal Ca2+ Absorption
Current Medicinal Chemistry Transcranial Direct Current Stimulation for Treatment of Alzheimer’s Disease: A Systematic Review of Randomized Clinical Trial
Current Psychiatry Reviews Memories are Made of This (Perhaps): A Review of Serotonin 5-HT6 Receptor Ligands and Their Biological Functions
Current Topics in Medicinal Chemistry