Abstract
As more and more protein sequences are available, homolog identification becomes increasingly important for functional, structural, and evolutional studies of proteins. Many homologous proteins were separated a very long time ago in their evolutionary history and thus their sequences share low sequence identity. These remote homologs have become a research focus in bioinformatics over the past decade, and some significant advances have been achieved. In this paper, we provide a comprehensive review on computational techniques used in remote homolog identification based on different methods, including sequence-sequence comparison, and sequence-structure comparison, and structure-structure comparison. Other miscellaneous approaches are also summarized. Pointers to the online resources of these methods and their related databases are provided. Comparisons among different methods in terms of their technical approaches, their strengths, and limitations are followed. Studies on proteins in SARS-CoV are shown as an example for remote homolog identification application.
Keywords: Remote homolog, homolog identification, evolution, sequence analysis, sequence profile, threading
Current Protein & Peptide Science
Title: Computational Methods for Remote Homolog Identification
Volume: 6 Issue: 6
Author(s): Xiu-Feng Wan and Dong Xu
Affiliation:
Keywords: Remote homolog, homolog identification, evolution, sequence analysis, sequence profile, threading
Abstract: As more and more protein sequences are available, homolog identification becomes increasingly important for functional, structural, and evolutional studies of proteins. Many homologous proteins were separated a very long time ago in their evolutionary history and thus their sequences share low sequence identity. These remote homologs have become a research focus in bioinformatics over the past decade, and some significant advances have been achieved. In this paper, we provide a comprehensive review on computational techniques used in remote homolog identification based on different methods, including sequence-sequence comparison, and sequence-structure comparison, and structure-structure comparison. Other miscellaneous approaches are also summarized. Pointers to the online resources of these methods and their related databases are provided. Comparisons among different methods in terms of their technical approaches, their strengths, and limitations are followed. Studies on proteins in SARS-CoV are shown as an example for remote homolog identification application.
Export Options
About this article
Cite this article as:
Wan Xiu-Feng and Xu Dong, Computational Methods for Remote Homolog Identification, Current Protein & Peptide Science 2005; 6 (6) . https://dx.doi.org/10.2174/138920305774933231
DOI https://dx.doi.org/10.2174/138920305774933231 |
Print ISSN 1389-2037 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5550 |
Call for Papers in Thematic Issues
Advancements in Proteomic and Peptidomic Approaches in Cancer Immunotherapy: Unveiling the Immune Microenvironment
The scope of this thematic issue centers on the integration of proteomic and peptidomic technologies into the field of cancer immunotherapy, with a particular emphasis on exploring the tumor immune microenvironment. This issue aims to gather contributions that illustrate the application of these advanced methodologies in unveiling the complex interplay ...read more
Artificial Intelligence for Protein Research
Protein research, essential for understanding biological processes and creating therapeutics, faces challenges due to the intricate nature of protein structures and functions. Traditional methods are limited in exploring the vast protein sequence space efficiently. Artificial intelligence (AI) and machine learning (ML) offer promising solutions by improving predictions and speeding up ...read more
Nutrition and Metabolism in Musculoskeletal Diseases
The musculoskeletal system consists mainly of cartilage, bone, muscles, tendons, connective tissue and ligaments. Balanced metabolism is of vital importance for the homeostasis of the musculoskeletal system. A series of musculoskeletal diseases (for example, sarcopenia, osteoporosis) are resulted from the dysregulated metabolism of the musculoskeletal system. Furthermore, metabolic diseases (such ...read more
Protein Folding, Aggregation and Liquid-Liquid Phase Separation
Protein folding, misfolding and aggregation remain one of the main problems of interdisciplinary science not only because many questions are still open, but also because they are important from the point of view of practical application. Protein aggregation and formation of fibrillar structures, for example, is a hallmark of a ...read more
Related Journals
- 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
Related Articles
-
Insulin-Like Growth Factor-1, a Potential Predicative Biomarker for Postoperative Delirium Among Elderly Patients with Open Abdominal Surgery
Current Pharmaceutical Design Information of ADME-Associated Proteins and Potential Application for Pharmacogenetic Prediction of Drug Responses
Current Pharmacogenomics Skin Regeneration: The Possibilities
Recent Patents on Regenerative Medicine A Single Fas Gene Mutation Changes Lupus Onset, Severity, Location, and Molecular Abnormalities in Mice
Current Molecular Medicine Food Fortification with Omega-3 Fatty Acids; Microencapsulation as an Addition Method
Current Nutrition & Food Science Drug Delivery Across the Blood-Brain Barrier
Current Drug Delivery Novel Guanosine Derivatives as Anti-HCV NS5b Polymerase: A QSAR and Molecular Docking Study
Medicinal Chemistry Combined Effect of Parthenolide and Various Anti-cancer Drugs or Anticancer Candidate Substances on Malignant Cells in vitro and in vivo
Mini-Reviews in Medicinal Chemistry Influence of Quaternary Conformation on the Biological Activities of the Asp49-phospholipases A2s from Snake Venoms
Protein & Peptide Letters Role of DPP4 and DPP4i in Glucose Homeostasis and Cardiorenal Syndrome
Endocrine, Metabolic & Immune Disorders - Drug Targets Direct and Indirect Antimicrobial Activities of Neuropeptides and their Therapeutic Potential
Current Protein & Peptide Science The Relevance of JAK2 in the Regulation of Cellular Transport
Current Medicinal Chemistry Cardiovascular Effects of Modulators of Soluble Guanylyl Cyclase Activity
Cardiovascular & Hematological Agents in Medicinal Chemistry Structure, Function, and Pathogenesis of SHP2 in Developmental Disorders and Tumorigenesis
Current Cancer Drug Targets The Design of Vectors for RNAi Delivery System
Current Pharmaceutical Design Endothelial Dysfunction in the Hypertensive State: Mechanisms of Hypertensive Cardiovascular Complications
Current Hypertension Reviews Cell Death: Tipping the Balance of Autoimmunity and Tissue Repair
Current Pharmaceutical Design Editorial (Thematic Issue: Medicinal Chemistry of Hepatitis C Virus: Current and Future Perspective)
Current Topics in Medicinal Chemistry PET Radioligands for In Vivo Visualization of Neuroinflammation
Current Pharmaceutical Design Sex Differences and Emerging New Risk Factors for Atherosclerosis and Its Thrombotic Complications
Current Pharmaceutical Design