Abstract
Background: Closely related to causes of various diseases such as rheumatoid arthritis, septic shock, and coeliac disease; tyrosine nitration is considered as one of the most important post-translational modification in proteins. Inside a cell, protein modifications occur accurately by the action of sophisticated cellular machinery. Specific enzymes present in endoplasmic reticulum accomplish this task. The identification of potential tyrosine residues in a protein primary sequence, which can be nitrated, is a challenging task.
Methods: To counter the prevailing, laborious and time-consuming experimental approaches, a novel computational model is introduced in the present study. Based on data collected from experimentally verified tyrosine nitration sites feature vectors are formed. Later, an adaptive training algorithm is used to train a back propagation neural network for prediction purposes. To objectively measure the accuracy of the proposed model, rigorous verification and validation tests are carried out.
Results: Through verification and validation, a promising accuracy of 88%, a sensitivity of 85%, a specificity of 89.18% and Mathew’s Correlation Coefficient of 0.627 is achieved.
Conclusion: It is concluded that the proposed computational model provides the foundation for further investigation and be used for the identification of nitrotyrosine sites in proteins.
Keywords: Nitrotyrosine, PseAAC, statistical moments, 5-step rule, prediction, rheumatoid arthritis.
Current Pharmaceutical Design
Title:pNitro-Tyr-PseAAC: Predict Nitrotyrosine Sites in Proteins by Incorporating Five Features into Chou’s General PseAAC
Volume: 24 Issue: 34
Author(s): Ahmad W. Ghauri, Yaser D. Khan, Nouman Rasool, Sher A. Khan*Kuo-Chen Chou
Affiliation:
- King Abdul Aziz University, Faculty of Computing and Information Technology in Rabigh, Jeddah, 21577,Saudi Arabia
Keywords: Nitrotyrosine, PseAAC, statistical moments, 5-step rule, prediction, rheumatoid arthritis.
Abstract: Background: Closely related to causes of various diseases such as rheumatoid arthritis, septic shock, and coeliac disease; tyrosine nitration is considered as one of the most important post-translational modification in proteins. Inside a cell, protein modifications occur accurately by the action of sophisticated cellular machinery. Specific enzymes present in endoplasmic reticulum accomplish this task. The identification of potential tyrosine residues in a protein primary sequence, which can be nitrated, is a challenging task.
Methods: To counter the prevailing, laborious and time-consuming experimental approaches, a novel computational model is introduced in the present study. Based on data collected from experimentally verified tyrosine nitration sites feature vectors are formed. Later, an adaptive training algorithm is used to train a back propagation neural network for prediction purposes. To objectively measure the accuracy of the proposed model, rigorous verification and validation tests are carried out.
Results: Through verification and validation, a promising accuracy of 88%, a sensitivity of 85%, a specificity of 89.18% and Mathew’s Correlation Coefficient of 0.627 is achieved.
Conclusion: It is concluded that the proposed computational model provides the foundation for further investigation and be used for the identification of nitrotyrosine sites in proteins.
Export Options
About this article
Cite this article as:
Ghauri W. Ahmad , Khan D. Yaser , Rasool Nouman , Khan A. Sher *, Chou Kuo-Chen , pNitro-Tyr-PseAAC: Predict Nitrotyrosine Sites in Proteins by Incorporating Five Features into Chou’s General PseAAC, Current Pharmaceutical Design 2018; 24 (34) . https://dx.doi.org/10.2174/1381612825666181127101039
DOI https://dx.doi.org/10.2174/1381612825666181127101039 |
Print ISSN 1381-6128 |
Publisher Name Bentham Science Publisher |
Online ISSN 1873-4286 |
Call for Papers in Thematic Issues
"Tuberculosis Prevention, Diagnosis and Drug Discovery"
The Nobel Prize-winning discoveries of Mycobacterium tuberculosis and streptomycin have enabled an appropriate diagnosis and an effective treatment of tuberculosis (TB). Since then, many newer diagnosis methods and drugs have been saving millions of lives. Despite advances in the past, TB is still a leading cause of infectious disease mortality ...read more
Current Pharmaceutical challenges in the treatment and diagnosis of neurological dysfunctions
Neurological dysfunctions (MND, ALS, MS, PD, AD, HD, ALS, Autism, OCD etc..) present significant challenges in both diagnosis and treatment, often necessitating innovative approaches and therapeutic interventions. This thematic issue aims to explore the current pharmaceutical landscape surrounding neurological disorders, shedding light on the challenges faced by researchers, clinicians, and ...read more
Emerging and re-emerging diseases
Faced with a possible endemic situation of COVID-19, the world has experienced two important phenomena, the emergence of new infectious diseases and/or the resurgence of previously eradicated infectious diseases. Furthermore, the geographic distribution of such diseases has also undergone changes. This context, in turn, may have a strong relationship with ...read more
Melanoma and Non-Melanoma Skin Cancer Treatment: Standard of Care and Recent Advances
In this thematic issue, we aim to provide a standard of care of the diagnosis and treatment of melanoma and non-melanoma skin cancer. The editor will invite authors from different countries who will write review articles of melanoma and non-melanoma skin cancers. The Diagnosis, Staging, Surgical Treatment, Non-Surgical Treatment all ...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
-
Regulation of Self-Reactive T Cells by Human Immunoglobulins- Implications for Multiple Sclerosis Therapy
Current Pharmaceutical Design Inflammation, Adipocytokines, and Atherosclerosis in the Metabolic Syndrome
Anti-Inflammatory & Anti-Allergy Agents in Medicinal Chemistry Small Molecule Antagonists of the Chemokine Receptor CCR5
Current Topics in Medicinal Chemistry Targeting of Antioxidant and Anti-Thrombotic Drugs to Endothelial Cell Adhesion Molecules
Current Pharmaceutical Design Curcumin: A Dietary Phytochemical for Targeting the Phenotype and Function of Dendritic Cells
Current Medicinal Chemistry Heparin Affin Regulatory Peptide: A New Target for Tumour Therapy?
Current Cancer Drug Targets Expression, Regulation and Function of Asporin, A Susceptibility Gene in Common Bone and Joint Diseases
Current Medicinal Chemistry Type I Interferon as a Target of Treatment in SLE
Endocrine, Metabolic & Immune Disorders - Drug Targets Mechanisms of Bone Erosion in Chronic Gout: Lessons Learned from Other Erosive Arthropathies
Current Rheumatology Reviews A Systematic Review of Drugs in Late-Stage Development for the Treatment of Multiple Sclerosis: A Focus on Oral Synthetic Drugs
Inflammation & Allergy - Drug Targets (Discontinued) Influence of Gender on C-Reactive Protein, Fibrinogen, and Erythrocyte Sedimentation Rate in Obstructive Sleep Apnea
Anti-Inflammatory & Anti-Allergy Agents in Medicinal Chemistry Antinuclear Antibodies and Lupus-like Manifestations in Rheumatoid Arthritis and Ankylosing Spondylitis Patients at 4 Months' Follow-up After Treatment with Infliximab and Etanercept
Current Rheumatology Reviews Re and Tc Complexes with Pyrazolyl-Containing Chelators: from Coordination Chemistry to Target-Specific Delivery of Radioactivity
Current Radiopharmaceuticals The Molecular Organization of Polymers of Cartilage in Health and Disease
Current Organic Chemistry The Peripheral Benzodiazepine Receptor: A Promising Therapeutic Drug Target
Current Medicinal Chemistry Arraying Autoantibodies in SLE – Lessons Learned
Current Molecular Medicine An Evidence-Based Review of the Mechanism of Action, Efficacy, and Safety of Biologic Therapies in the Treatment of Psoriasis and Psoriatic Arthritis
Current Medicinal Chemistry Estrogen, A Double-Edged Sword: Modulation of TH1- and TH2-Mediated Inflammations by Differential Regulation of TH1 / TH2 Cytokine Production
Current Drug Targets - Inflammation & Allergy Modulation of Apoptosis: New Opportunities for Drug Discovery to Treat Autoimmune Thyroiditis
Recent Patents on Inflammation & Allergy Drug Discovery Alkannins and Shikonins: A New Class of Wound Healing Agents
Current Medicinal Chemistry