Combinatorial Chemistry & High Throughput Screening - Volume 12, Issue 5, 2009

Computer-assisted drug design is used to increase the chances of finding valuable drug candidates, by applying a wide range of computational methods, such as machine learning, structure-activity relationships, quantitative structure-activity relationships, molecular mechanics, quantum mechanics, molecular dynamics, and drug-protein docking. Machine learning is an important field of artificial intelligence, and includes a Read More

A large number of different machine learning methods can potentially be used for ligand-based virtual screening. In our contribution, we focus on three specific nonlinear methods, namely support vector regression, Gaussian process models, and decision trees. For each of these methods, we provide a short and intuitive introduction. In particular, we will also discuss how confidence estimates (error bars) can be obtained from Read More

Naive Bayesian classifiers are a relatively recent addition to the arsenal of tools available to computational chemists. These classifiers fall into a class of algorithms referred to broadly as machine learning algorithms. Bayesian classifiers may be used in conjunction with classical modeling techniques to assist in the rapid virtual screening of large compound libraries in a systematic manner with a minimum of human interve Read More

We present here the random forest supervised machine learning algorithm applied to flexible docking results from five typical virtual high throughput screening (HTS) studies. Our approach is aimed at: i) reducing the number of compounds to be tested experimentally against the given protein target and ii) extending results of flexible docking experiments performed only on a subset of a chemical library in order to selec Read More

Increasing concern is being shown by the scientific community, government regulators, and the public about endocrine-disrupting chemicals that, in the environment, are adversely affecting human and wildlife health through a variety of mechanisms, mainly estrogen receptor-mediated mechanisms of toxicity. Because of the large number of such chemicals in the environment, there is a great need for an effective mean Read More

Among the absorption, distribution, metabolism, elimination, and toxicity properties (ADMET), unfavorable oral bioavailability is indeed an important reason for stopping further development of the drug candidates. Thus, predictions of oral bioavailability and bioavailability-related properties, especially intestinal absorption are areas in need of progress to aid pharmaceutical drug development. In this article, we review recent Read More

Accurate classification of instances depends on identification and removal of redundant features. Classification of data having high dimensionality is usually performed in conjunction with an appropriate feature selection method. Feature selection enables identification of the most informative feature subset from the enormously vast search space that can accurately classify the given data. We propose an ant colony optimizatio Read More

Feature selection is an important challenge in many classification problems, especially if the number of features greatly exceeds the number of examples available. We have developed a procedure - GenForest - which controls feature selection in random forests of decision trees by using a genetic algorithm. This approach was tested through our entry into the Comparative Evaluation of Prediction Algorithms 2006 (CoEPrA) Read More

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Establishment of a saliva protein/peptide signature will provide important information for clinical diagnostics and prognosis of human disease. We digested human whole saliva with trypsin to create a tryptic digest salivary peptidome. Proteins/peptides were subsequently identified by high throughput tandem mass spectrometry in conjunction with database searching. Sixty-three saliva peptides corresponding to twenty-two Read More

In living organisms, heme is an essential molecule for various biological functions. Recent studies also suggest that heme functions as organelle-derived signal that regulates fundamental cell processes. Furthermore, estimation of heme is widely used for studying various blood disorders. In this regard, development of a rapid, sensitive, and high throughput heme assay has been sought. The most frequently used method of Read More

A novel three-component, one-pot condensation of the zwitterion generated from dialkyl acetylenedicarboxylate and isocyanides with homophthalic anhydride is described. The reaction affords new 6-oxopyrano[2,3- c]isochromenes in good yield. Isochromenes have been reported to possess diverse biological activities such as antibacterial, antifungal, antiinflammatory, and antiangiogenic effects. Moreover, Theses important c Read More