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183 articles for “Protein-protein interactions”
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Introduction to Biological Networks and their Contributions to Systems Biology
Abstract: Biological networks provide a conceptual framework to represent and analyze the intricate interconnections among the numerous components that make up living systems. This review paper elucidates the foundational principles of networks and their diverse applications in systems biology, highlighting their crucial role in understanding the inherent complexity of biological processes. Utilizing graph theory, these networks represent entities like genes, proteins, and metabolites as nodes, with their interactions depicted as edges. …
Published in International Journal of Bioinformatics and Computational Biology · Vol. 2, Issue 1, 2024 · pp. 53–70 Read article
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Computational Simulations in Drug Discovery: Modeling Protein Folding and Drug Binding
Abstract: Computational simulations have become essential tools in drug discovery, offering unprecedented insights into molecular behavior at the atomic level. These simulations, particularly in the domains of protein folding and drug binding, allow for the exploration of complex biological systems that are often difficult to study experimentally. Protein folding, a critical aspect of drug discovery, involves the transition of a polypeptide chain from an unfolded to a biologically active structure. Understanding …
Published in Research and Reviews : Journal of Computational Biology · Vol. 14, Issue 1, 2025 · pp. 23–29 Read article
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Exploring Oroxylum indicum Phytochemicals as VEGFR-2 Inhibitors: A Molecular Docking Approach for Cancer Management
Abstract: Cancer is still a major health problem around the world and is one of the top causes of death. A protein called VEGFR-2 (vascular endothelial growth factor receptor 2) is important because it helps blood vessels grow by supporting the survival, movement, and growth of certain cells. This process is essential for tumors to grow and spread to other parts of the body. This study focused on evaluating the binding …
Published in International Journal of Cell Biology and Cellular Functions · Vol. 3, Issue 2, 2025 · pp. 48–62 Read article
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Experimental Studies and in silico Analysis on Quarum Sensing and System Simulation in Pseudomonas aeruginosa
Abstract: Pseudomonas aeruginosa is the most common pathogenic bacterium present in human microbial flora, biofilms, soil and water associated and support self microbial communications and survilance. The present study shows estimated protein concentration present in two days grown in Mullar hinton broth was resulted around 32.5 mg/ml. The studies in protein interaction on X-ray film with aqueous fruit and vegetable extracts showed good results with apple, straw berry, cucumber, grape, orrange, …
Published in Research and Reviews : Journal of Computational Biology · Vol. 7, Issue 1, 2018 · pp. 1–8 Read article
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The Role of Quercetin, Curcumin, Eugenol, and Andrographolide in COVID-19 Treatment: A Review of Their Mechanisms of Action and Clinical Efficacy
Abstract: The world has recently experienced the covid diseases. It became the global worry with no remedy initially. Later, different antiviral medications in the form of injections and nasal sprays began to be employed. Many studies have been conducted to determine the antiviral effects of phytochemical substances. The corona virus's spike protein interacts with the ACE2 receptors on the alveoli's surface to enter the cell. After that, the polyprotein is transformed …
Published in Research and Reviews : A Journal of Biotechnology · Vol. 13, Issue 1, 2023 · pp. 27–38 Read article
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Biochemical and Structural Characterization of Helicobacter pylori Peptide deformylase by Computational Methods
Abstract: Helicobacter pylorus is classified as class one carcinogen in causing gastric cancer. Peptide deformylases (PDFs) present in bacteria removes the formyl group from the N-terminal Methionine of newly synthesized proteins which is necessary in protein maturation. These enzymes have shown as new targets in antibacterial, antimalarial and anticancer drug discovery. Here an insilico technique was initiated to characterize structural and biochemical properties of this protein. Pair wise sequence alignment with …
Published in Research & Reviews: A Journal of Bioinformatics · Vol. 4, Issue 3, 2017 · pp. 22–28 Read article
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Advanced Computational Models for Predicting Molecular Interactions
Abstract: Understanding molecular interactions is essential for a number of disciplines, including biochemistry, materials science, and medication development. Traditional experimental methods, while accurate, are often time-consuming and expensive. Advanced computational models have emerged as powerful tools to predict molecular interactions efficiently. In order to predict the behavior and interactions of molecules at the atomic and subatomic levels, this paper reviews the most recent developments in computational techniques, such as machine learning …
Published in International Journal of Advance in Molecular Engineering · Vol. 2, Issue 1, 2024 · pp. 8–13 Read article
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Neuro-Symbolic Agentic AI for Autonomous Scientific Discovery: Integrating Deep Reinforcement Learning, Quantum Simulation, and XAI-Audited LLM Hypothesis Generation in Drug Target Identification
Abstract: The exponential growth of multi-omics data and the increasing complexity of disease-associated protein interactomes have rendered conventional drug target identification pipelines computationally and epistemologically inadequate. This paper presents the Neuro-Symbolic Agentic AI for Scientific Discovery (NS-AASD) framework, a unified architecture that cohesively integrates deep reinforcement learning (DRL) exploration strategies, variational quantum simulation (VQS) of protein conformational dynamics, and XAI-audited large language model (LLM) hypothesis generation within an autonomous scientific discovery …
Published in Research and Reviews : Journal of Computational Biology · Vol. 15, Issue 2, 2026 · pp. 15–24 Read article
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Integrating Network Pharmacology and Molecular Docking to Investigate Boerhavia diffusa for Pancreatic Cancer Treatment
Abstract: Objective: In this study, network pharmacology was applied to determine the therapeutic effects of the bioactive compounds of Boerhavia diffusa. Network pharmacology can unearth the underlying mechanisms between drugs and the disease targets and aids in the discovery of novel medications for complex conditions such as cancer. Methods: To predict the molecular mechanisms of action of Boerhavia diffusa in the treatment of was screened using the GeneCards database. The Venn …
Published in International Journal of Molecular Biotechnological Research · Vol. 2, Issue 1, 2024 · pp. 29–49 Read article
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Sequence analysis, DNA Methylation and Molecular therapy of Oral cancer caused by Human Papilloma Virus
Abstract: DNA methylations with oral cancer are been associated with high-risk Human Papillomavirus (HPV) and Epstein-Barr Virus (EBV) onco-proteins interactions may cooperate to increase disease severity. The work focused on human papillomavirus strain 16, a high-risk, sexually transmitted responsible for 95% of all cervical cancers and a large portion of oropharyngeal cancers. The prediction of genes from has shown seven genes from HPV16 strain. Based on gene identification studies, Human papilloma …
Published in International Journal of Cell Biology and Cellular Functions · Vol. 4, Issue 2, 2026 · pp. 1–9 Read article
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InSilico Analysis and Homology Modeling of Tetrahydroprotoberberine Oxide involved in the Berberine Biosynthesis
Abstract: Objective: Berberine, a bioactive compound found in various plant species, exhibits diverse pharmacological properties with potential applications in pharmaceutical research. The biosynthesis of berberine involves several enzymatic steps, with (S)-tetrahydroprotoberberine oxidase playing a pivotal role. This study aimed to elucidate the structural and functional characteristics of (S)-tetrahydroprotoberberine oxidase to better understand its role in berberine biosynthesis and its potential biotechnological applications. Methods: Using bioinformatics tools and computational methods, the physicochemical …
Published in Emerging Trends in Metabolites · Vol. 1, Issue 1, 2024 · pp. 7–26 Read article
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“Evaluation of superoxide Dismutase (SOD) enzyme level and some indicators in people exposed to smoke”
Abstract: The aim of this study is to assess the level of SOD enzyme and its impact in people who are exposed to smoking, in addition to measuring C-interactive protein, and finally measure a complete picture of blood samples taken from patients. The results of the current study showed there is a significant differences (p<0.05) in the activity of the SOD. The mean of SOD activity in patient was 127.9 U/ml …
Published in International Journal of Toxins and Toxics · Vol. 1, Issue 2, 2024 · pp. 52–55 Read article
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In Silico Study of Curcumin-Sugar Conjugates as Dual Inhibitors on Both COX-1 and COX-2 Enzymes for the Discovery of Anti-inflammatory Agents
Abstract: Curcumin is a polyphenolic compound well known for its anti-inflammatory properties. The aim of the study was to design some novel curcumin derivatives that are water soluble as well as good anti-inflammatory agents with fewer side effects. In silico study was performed on the proteins by using three softwares iGEMDOCK, AutoDOCK, AutoDOCKVina as dual inhibitors for both COX-1 and COX-2. The result gives us theoretical contribution for understanding the ligand-protein …
Published in Research & Reviews: A Journal of Bioinformatics · Vol. 4, Issue 1, 2017 · pp. 25–30 Read article
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Molecular Docking-Based Analysis of Rauvolfia serpentina Alkaloids Targeting HPV E1 and L1 Proteins for Antiviral Therapeutic Potential
Abstract: Human papillomavirus (HPV) is a major cause of cervical cancer and other epithelial cancers. E1 and L1 proteins are crucial to the virus's lifespan. E1 is a viral helicase that is needed for HPV DNA replication, and L1 is the main structural capsid protein that builds the virion and infects target cells. Going after these proteins is a good way to stop viruses from spreading. In this case, Rauvolfia serpentina, …
Published in Research and Reviews: A Journal of Pharmaceutical Science · Vol. 17, Issue 1, 2026 · pp. 100–113 Read article
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Exploring Potential Phytochemicals for Myasthenia Gravis Treatment: A Molecular Docking and ADME Analysis Approach
Abstract: Objective: Muscle feebleness and exhaustion derived from a disruption in neuromuscular transference are hallmarks of the crippling autoimmune disease myasthenia gravis (MG). The drawbacks of the current MG therapy options are frequently partial efficacy and adverse effects. To investigate the potential of phytochemicals in MG control, in this work we integrated molecular docking with ADME (absorption, distribution, metabolism, and excretion) analysis using a computer method. We identified molecules exhibiting favorable …
Published in International Journal of Molecular Biotechnological Research · Vol. 2, Issue 2, 2024 · pp. 1–13 Read article
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Insilico 3D Structure Modeling and Docking to Find Potent Inhibitors for Thrombocytopenia
Abstract: Lots of people are getting affected by various kinds of auto-immune disease in their day to day life and thrombocytopenia is one of them, which occurs due to lack of thrombocytes or platelets. Various kinds of vaccines, drugs are used to stop the disease, but the effect varies from person to person depending upon the immune system. In thrombocytopenia disease the integrin beta protein of human affects the person’s own …
Published in Research & Reviews: A Journal of Bioinformatics · Vol. 1, Issue 3, 2014 · pp. 31–40 Read article
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Comparative Proteomics: From Cell Lines to Clinical Samples
Abstract: Comparative proteomics is a powerful tool for understanding the molecular differences between various biological samples. It entails identifying and measuring proteins in complex biological samples to assess their abundance, modifications, and interactions under various conditions. This approach plays a crucial role in advancing biomedical research, especially in disease understanding, biomarker discovery, and therapeutic development. While cell lines are widely used for proteomic studies due to their controlled environments and reproducibility, …
Published in Research and Reviews : Journal of Computational Biology · Vol. 13, Issue 3, 2024 · pp. 30–34 Read article
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In-Silico Docking of Rubia cordifolia Phytocompounds as Potential MMP-2 Inhibitors for Varicose Vein Management
Abstract: Varicose veins are one of the most common disorders, affecting the vein structure and function of lower limbs, yet there has been no absolute cure found yet. One of the underlying causes for worsening of the condition is the proteolytic activity of MMPs which are a group of enzymes that affect the extracellular matrix (ECM) surrounding the affected veins. Phytocompounds of Rubia cordifolia (Manjishta) were docked against the MMP-2 protein …
Published in International Journal of Biochemistry and Biomolecule Research · Vol. 3, Issue 2, 2025 · pp. 31–42 Read article
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HDAC and HDAC Inhibitors: Implication in Different Pathological Ailments
Abstract: Histone deacetylases (HDAC) and its inhibitors have been found implicated in various diseased conditions. HDACs regulate the histone tail, chromatin conformation, protein-DNA interaction, and even transcription. They have also been found to regulate the post translational modifications through deacetylation of proteins, and hence are involved in many pathophysiological conditions. Till date, USFDA has approved vorinostat, romidepsin, panobinostat, and belinostat as HDAC inhibitors for the treatment of cancer. Considering their wide …
Published in Research & Reviews: A Journal of Drug Design & Discovery · Vol. 5, Issue 3, 2018 · pp. 35–40 Read article
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Investigating Curcumin Phytocompounds as Prospective Parkinson's Disease Therapeutic Agents: A Computational Method that Targets LRRK2 Protein
Abstract: Objective: Parkinson’s Disease is the second stage predominant neurodegenerative illness. Primary aetiology is still unknown. One of the biggest battlegrounds in modern medicine is discovering the cause of Parkinson’s disease (PD), as well as the hunt for palliative treatments and, if feasible, a cure. The objective of this work is to identify the phytocompounds from curcumin (curcuma longa) for the treatment of PD. Curcumin, a well-researched phytochemical, has been suggested …
Published in Research and Reviews : Journal of Computational Biology · Vol. 12, Issue 3, 2023 · pp. 55–67 Read article