Biomaterial Database

Troubleshooting computational methods in drug discovery. 2010

Sandhya Kortagere, and Sean Ekins

Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA. sandhya.kortagere@DrexelMed.edu

Computational approaches for drug discovery such as ligand-based and structure-based methods, are increasingly seen as an efficient approach for lead discovery as well as providing insights on absorption, distribution, metabolism, excretion and toxicity (ADME/Tox). What is perhaps less well known and widely described are the limitations of the different technologies. We have therefore presented a troubleshooting approach to QSAR, homology modeling, docking as well as hybrid methods. If such computational or cheminformatics methods are to become more widely used by non-experts it is critical that such limitations are brought to the user's attention and addressed during their workflows. This could improve the quality of the models and results that are obtained.

UI	MeSH Term	Description	Entries
D011237	Predictive Value of Tests	In screening and diagnostic tests, the probability that a person with a positive test is a true positive (i.e., has the disease), is referred to as the predictive value of a positive test; whereas, the predictive value of a negative test is the probability that the person with a negative test does not have the disease. Predictive value is related to the sensitivity and specificity of the test.	Negative Predictive Value,Positive Predictive Value,Predictive Value Of Test,Predictive Values Of Tests,Negative Predictive Values,Positive Predictive Values,Predictive Value, Negative,Predictive Value, Positive
D003198	Computer Simulation	Computer-based representation of physical systems and phenomena such as chemical processes.	Computational Modeling,Computational Modelling,Computer Models,In silico Modeling,In silico Models,In silico Simulation,Models, Computer,Computerized Models,Computer Model,Computer Simulations,Computerized Model,In silico Model,Model, Computer,Model, Computerized,Model, In silico,Modeling, Computational,Modeling, In silico,Modelling, Computational,Simulation, Computer,Simulation, In silico,Simulations, Computer
D004353	Drug Evaluation, Preclinical	Preclinical testing of drugs in experimental animals or in vitro for their biological and toxic effects and potential clinical applications.	Drug Screening,Evaluation Studies, Drug, Pre-Clinical,Drug Evaluation Studies, Preclinical,Drug Evaluations, Preclinical,Evaluation Studies, Drug, Preclinical,Evaluation, Preclinical Drug,Evaluations, Preclinical Drug,Medicinal Plants Testing, Preclinical,Preclinical Drug Evaluation,Preclinical Drug Evaluations,Drug Screenings,Screening, Drug,Screenings, Drug
D004364	Pharmaceutical Preparations	Drugs intended for human or veterinary use, presented in their finished dosage form. Included here are materials used in the preparation and/or formulation of the finished dosage form.	Drug,Drugs,Pharmaceutical,Pharmaceutical Preparation,Pharmaceutical Product,Pharmaceutic Preparations,Pharmaceutical Products,Pharmaceuticals,Preparations, Pharmaceutical,Preparation, Pharmaceutical,Preparations, Pharmaceutic,Product, Pharmaceutical,Products, Pharmaceutical
D006801	Humans	Members of the species Homo sapiens.	Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000818	Animals	Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA.	Animal,Metazoa,Animalia
D014116	Toxicology	The science concerned with the detection, chemical composition, and biological action of toxic substances or poisons and the treatment and prevention of toxic manifestations.	Toxinology,Evidence Based Toxicology,Evidence-Based Toxicology,Based Toxicologies, Evidence,Based Toxicology, Evidence,Evidence Based Toxicologies,Evidence-Based Toxicologies,Toxicologies, Evidence Based,Toxicologies, Evidence-Based,Toxicology, Evidence Based,Toxicology, Evidence-Based
D055808	Drug Discovery	The process of finding chemicals for potential therapeutic use.	Drug Prospecting,Discovery, Drug,Prospecting, Drug
D018675	Toxicity Tests	An array of tests used to determine the toxicity of a substance to living systems. These include tests on clinical drugs, foods, and environmental pollutants.	Tests, Toxicity,Test, Toxicity,Toxicity Test
D019295	Computational Biology	A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.	Bioinformatics,Molecular Biology, Computational,Bio-Informatics,Biology, Computational,Computational Molecular Biology,Bio Informatics,Bio-Informatic,Bioinformatic,Biologies, Computational Molecular,Biology, Computational Molecular,Computational Molecular Biologies,Molecular Biologies, Computational