Motivation: The output of a bioinformatic tool such as BLAST must usually be interpreted by an expert before reliable conclusions can be drawn. This may be based upon the expert's experience, additional data and statistical analysis. Often the process is laborious, goes unrecorded and may be biased. Argumentation is an established technique for reasoning about situations where absolute truth or precise probability is impossible to determine.
Results: We demonstrate the application of argumentation to 3D-PSSM, a protein structure prediction tool. The expert's interpretation of results is represented as an argumentation framework. Given a 3D-PSSM result, an automated procedure constructs arguments for and against the conclusion that the result is a good predictor of protein structure. In addition to capturing the unique expertise of the author of 3D-PSSM for distribution to users, an improvement in recall of 5-10 percentage points is achieved. This technique can be applied to a wide range of bioinformatic tools.
Availability: Example public server and benchmarking data are available at http://www.sbg.bio.ic.ac.uk/~brj03/argumentation/paper/. Source code available on request.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1093/bioinformatics/btl018 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Small Molecular Oligopeptides Adorned with Tryptophan Residues as Potent Antitumor Agents: Design, Synthesis, Bioactivity Assay, Computational Prediction, and Experimental Validation.
J Chem Inf Model
January 2025
Key Laboratory for Photonic and Electronic Bandgap Materials, Ministry of Education, College of Chemistry and Chemical Engineering, Harbin Normal University, Harbin 150025, China.
Tryptophan participates in important life activities and is involved in various metabolic processes. The indole and aromatic binuclear ring structure in tryptophan can engage in diverse interactions, including π-π, π-alkyl, hydrogen bonding, cation-π, and CH-π interactions with other side chains and protein targets. These interactions offer extensive opportunities for drug development.
View Article and Find Full Text PDFCordycepin and Its Structural Derivatives Effectively Suppress the High Expression of Epidermal Growth Factor Receptor (EGFR) Tyrosine Kinase in Breast Carcinomas: A Computational Drug Development Approach.
Curr Med Chem
January 2025
Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
Background: Breast cancer is a frequently diagnosed malignant disease and the primary cause of mortality among women with cancer worldwide. The therapy options are influenced by the molecular subtype due to the intricate nature of the condition, which consists of various subtypes. By focusing on the activation of receptors, Epidermal Growth Factor Receptor (EGFR) tyrosine kinase can be utilized as an effective drug target for therapeutic purposes of breast cancer.
View Article and Find Full Text PDFComputational Model to Predict Potential Therapeutic Targets Employing Generative Adversarial Networks for Analysis of Proteins Involved in Mycobacterium fortuitum Biofilm Formation.
Curr Med Chem
January 2025
Department of Electronics & Communication Engineering, Jaypee University of Information Technology, Solan, H.P., India.
A planktonic population of bacteria can form a biofilm by adhesion and colonization. Proteins known as "adhesins" can bind to certain environmental structures, such as sugars, which will cause the bacteria to attach to the substrate. Quorum sensing is used to establish the population is dense enough to form a biofilm.
View Article and Find Full Text PDFDelineating CYP2C19-Mediated Interactions: Network Pharmacology Investigation of Ilaprazole and Clopidogrel versus Conventional Proton Pump Inhibitors.
Curr Drug Discov Technol
December 2024
Department of Pharmacy Practice, SRM College of Pharmacy, SRM Institute of Science and Technology, Kattankulathur, Chengalpattu District, Tamilnadu, 603203, India.
Background: Clopidogrel, an antiplatelet drug commonly used in cardiovascular disease, is metabolized by the liver mainly through CYP2C19. Concomitant use of Proton pump inhibitors along with clopidogrel may affect the potency of clopidogrel by CYP2C19 inhibition. However, a novel PPI, ilaprazole is known to differ in its pharmacokinetic features, given the potential differences between ilaprazole's interactions and their metabolism with clopidogrel.
View Article and Find Full Text PDFMolecular Balances as Physical Organic Chemistry Tools to Quantify Noncovalent Interactions.
Chemistry
January 2025
Institute of Chemical Research of Catalonia: Institut Catala d'Investigacio Quimica, -, Av. Països Catalans 16, 43007, Tarragona, SPAIN.
Noncovalent interactions are present in numerous synthetic and biological systems, playing an essential role in vital processes for life such as stabilization of proteins' structures or reversible binding in substrate-receptor complexes. Their study is relevant, but it presents challenges due to its inherent weak nature. In this context, molecular balances (MBs) are one of the most efficient physical organic chemistry tools to quantify noncovalent interactions, bringing beneficial knowledge regarding their nature and strength.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!