Abstract
The rapid increase in experimental data along with recent progress in computational methods has brought modern biology a step closer toward solving one of the most challenging problems: prediction of protein function. Comprehension of protein function at its most basic level requires understanding of molecular interactions. Currently, it is becoming universally accepted that the scale of the accumulated data for analysis and for prediction necessitate highly efficient computational tools with appropriate application capabilities. The review presents the up-to-date advances in computational methods for structural pattern discovery and for prediction of molecular associations. We focus on their applications toward a range of biological problems and highlight the advantages of the combination of these methods and their integration with biological experiments. We provide examples, synergistically merging structural modeling, rigid and flexible structural alignment and detection of conserved structural patterns and docking (rigid and flexible with hinge-bending movements). We hope the review will lead to a broader utilization of computational methods, and their cross-fertilization with experiment.
Keywords: structural pattern discovery, structural genomics, structure comparison, structural alignment, docking, drug design, conservation, flexible structural alignment, flexible docking, multiple structural alignment
Current Protein & Peptide Science
Title: From Structure to Function: Methods and Applications
Volume: 6 Issue: 2
Author(s): Haim J. Wolfson, Maxim Shatsky, Dina Schneidman-Duhovny, Oranit Dror, Alexandra Shulman-Peleg, Buyong Ma and Ruth Nussinov
Affiliation:
Keywords: structural pattern discovery, structural genomics, structure comparison, structural alignment, docking, drug design, conservation, flexible structural alignment, flexible docking, multiple structural alignment
Abstract: The rapid increase in experimental data along with recent progress in computational methods has brought modern biology a step closer toward solving one of the most challenging problems: prediction of protein function. Comprehension of protein function at its most basic level requires understanding of molecular interactions. Currently, it is becoming universally accepted that the scale of the accumulated data for analysis and for prediction necessitate highly efficient computational tools with appropriate application capabilities. The review presents the up-to-date advances in computational methods for structural pattern discovery and for prediction of molecular associations. We focus on their applications toward a range of biological problems and highlight the advantages of the combination of these methods and their integration with biological experiments. We provide examples, synergistically merging structural modeling, rigid and flexible structural alignment and detection of conserved structural patterns and docking (rigid and flexible with hinge-bending movements). We hope the review will lead to a broader utilization of computational methods, and their cross-fertilization with experiment.
Export Options
About this article
Cite this article as:
Wolfson J. Haim, Shatsky Maxim, Schneidman-Duhovny Dina, Dror Oranit, Shulman-Peleg Alexandra, Ma Buyong and Nussinov Ruth, From Structure to Function: Methods and Applications, Current Protein & Peptide Science 2005; 6 (2) . https://dx.doi.org/10.2174/1389203053545435
DOI https://dx.doi.org/10.2174/1389203053545435 |
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
-
“Epileptic Encephalopathy” of Infancy and Childhood: Electro-Clinical Pictures and Recent Understandings
Current Neuropharmacology Editorial: DSM-5 and the Challenge of Understanding and Treating Adolescents
Adolescent Psychiatry Homocysteine Level and Mechanisms of Injury in Parkinson's Disease as Related to MTHFR, MTR, and MTHFD1 Genes Polymorphisms and LDopa Treatment
Current Genomics Small Ruminant Lentiviruses and Human Immunodeficiency Virus: Cousins that Take a Long View
Current HIV Research Ligand-Based Peptide Design and Combinatorial Peptide Libraries to Target G Protein-Coupled Receptors
Current Pharmaceutical Design Insight into the Role of Photoreception and Light Intervention for Sleep and Neuropsychiatric Behaviour in the Elderly
Current Alzheimer Research Bioactivity of Hybrid Polymeric Magnetic Nanoparticles and Their Applications in Drug Delivery
Current Pharmaceutical Design Lung Ultrasound in the Critically Ill Neonate
Current Pediatric Reviews HCV-Related Central and Peripheral Nervous System Demyelinating Disorders
Inflammation & Allergy - Drug Targets (Discontinued) Therapeutic Targeting of TRPV1 by Resiniferatoxin, from Preclinical Studies to Clinical Trials
Current Topics in Medicinal Chemistry Regular Physical Activity and Vascular Aging
Current Pharmaceutical Design Endocannabinoids in the Central Nervous System: From Neuronal Networks to Behavior
Current Drug Targets - CNS & Neurological Disorders A Brief History of ‘Lone’ Atrial Fibrillation: From ‘A Peculiar Pulse Irregularity’ to a Modern Public Health Concern
Current Pharmaceutical Design Advanced Tools of Regenerative Medicine for Neurodegenerative Diseases
Recent Patents on Regenerative Medicine Molecular Players at the Intersection of Obesity and Osteoarthritis
Current Drug Targets Lipid Membranes and β-Amyloid: A Harmful Connection
Current Protein & Peptide Science Multi- and Inter-Disciplinary Science in Personalized Delivery of Stem Cells for Tissue Repair
Current Stem Cell Research & Therapy Preclinical Pharmacology of mGlu2 / 3 Receptor Agonists: Novel Agents for Schizophrenia?
Current Drug Targets - CNS & Neurological Disorders Gene Therapy for Neurological Disorders: Challenges and Future Prospects for the Use of Growth Factors for the Treatment of Parkinsons Disease
Current Gene Therapy Mood, Memory and Movement: An Age-Related Neurodegenerative Complex?
Current Aging Science