Quantifying intrinsic specificity: A potential complement to affinity in drug screening

We report here the investigation of a novel description of specificity in protein-ligand binding based on energy landscape theory. We define a new term, intrinsic specificity ratio (ISR), which describes the level of discrimination in binding free energies of the native basin for a protein-ligand complex from the weaker binding states of the same ligand. We discuss the relationship between the intrinsic specificity we defined here and the conventional definition of specificity. In a docking study of molecules with the enzyme COX-2, we demonstrate a statistical correspondence between ISR value and geometrical shapes of the small molecules binding to COX-2. We further observe that the known selective (nonselective) inhibitors of COX-2 have higher (lower) ISR values. We suggest that intrinsic specificity ratio may be a useful new criterion and a complement to affinity in drug screening and in searching for potential drug lead compounds.

Molecular docking and 3D-QSAR study of pyranmycin derivatives against 16S rRNA A site

To understand pharmacophore properties of pyranmycin derivatives and to design novel inhibitors of 16S rRNA A site, comparative molecular field analysis (CoMFA) approach was applied to analyze three-dimensional quantitative structure-activity relationship (3D-QSAR) of 17 compounds. AutoDock 3.0.5 program was employed to locate the orientations and conformations of the inhibitors interacting with 16S rRNA A site. The interaction mode was demonstrated in the aspects of inhibitor conformation, hydrogen bonding and electrostatic interaction. Similar binding conformations of these inhibitors and good correlations between the calculated binding free energies and experimental biological activities suggest that the binding conformations of these inhibitors derived from docking procedure were reasonable. Robust and predictive 3D-QSAR model was obtained by CoMFA with q(2) values of 0.723 and 0.993 for cross-validated and noncross-validated, respectively. The 3D-QSAR model built here will provide clear guidelines for novel inhibitors design based on the Pyranmycin derivatives against 16S rRNA A site. (c) 2005 Elsevier B.V. All rights reserved.

automated test case generation for the stress testing of multimedia systems

With the advancement in network bandwidth and computing power, multimedia systems have become a popular means for information delivery. However, general principles of system testing cannot be directly applied to testing of multimedia systems on account of their stringent temporal and synchronization requirements. In particular, few studies have been made on the stress testing of multimedia systems with respect to their temporal requirements under resource saturation. Stress testing is important because erroneous behavior is most likely to occur under resource saturation. This paper presents an automatable method of test case generation for the stress testing of multimedia systems. It adapts constraint solving techniques to generate test cases that lead to potential resource saturation in a multimedia system. Coverage of the test cases is defined upon the reachability graph of a multimedia system. The proposed stress testing technique is supported by tools and has been successfully applied to a real-life commercial multimedia system. Although our technique focuses on the stress testing of multimedia systems, the underlying issues and concepts are applicable to other types of real-time systems.

Validation and in situ application of an automated dissolved nickel monitor for estuarine studies

The validation of a fully automated dissolved Ni monitor for in situ estuarine studies is presented, based on adsorptive cathodic stripping voltammetry (AdCSV). Dissolved Ni concentrations were determined following on-line filtration and UV digestion, and addition of an AdCSV ligand (dimethyl glyoxime) and pH buffer (N-2-hydroxyethylpiperazine-N′-2-ethanesulphonic acid). The technique is capable of up to six fully quantified Ni measurements per hour. The automated in situ methodology was applied successfully during two surveys on the Tamar estuary (south west Britain). The strongly varying sample matrix encountered in the estuarine system did not present analytical interferences, and each sample was quantified using internal standard additions. Up to 37 Ni measurements were performed during each survey, which involved 13 h of continuous sampling and analysis. The high resolution data from the winter and summer tidal cycle studies allowed a thorough interpretation of the biogeochemical processes in the studied estuarine system.

Automated voltammetric system for shipboard determination of metal speciation in sea water

An automated and semi-intelligent voltammetric system is described for trace metal analysis. The system consists of a voltammeter interfaced with a personal computer, a sample changer, 2 peristaltic pumps, a motor burette and a hanging mercury drop electrode. The system carries out fully automatically approximately 5 metal determinations per hour (including at least 3 repetitive scans and calibration by standard addition) at trace levels encountered in clean sea water. The computer program decides what level of standard addition to use and evaluates the data prior to switching to the next sample. Alternatively, the system can be used to carry out complexing ligand titration with copper whilst recording the labile copper concentration; in this mode up to 8 full titrations are carried out per day. Depth profiles for chromium speciation in the Mediterranean Sea and a profile for copper complexing ligand concentrations in the North Atlantic Ocean measured on board-ship with the system are presented. The chromium speciation was determined using a new method to differentiate between Cr(III) and Cr(VI) utilizing adsorption of Cr(III) on silica particles.

automated test program generation for an industrial optimizing compiler

Association for Computing Machinery, ACM; IEEE; IEEE Computer Society; SIGSOFT

The algorithm on automated aromaticity perception of molecules

It is important to detect the aromaticity of structures during the process of structure elucidation and output. In this paper, an alogrithm was proposed to detect the aromaticity of structures by the use of algorithm on ring identification. The results show that it could be used to identify most of the aromatic structure. It have been used as constraints of Expert System on Elucidation Structure of Organic Compounds(ESESOC) and a good result has been achieved.

Rapid automated in-situ monitoring of total dissolved iron and total dissolved manganese in underground water by reverse-flow injection with chemiluminescence detection during the process of water treatment

Measurement of iron and manganese is very important in evaluating the quality of natural waters. We have constructed an automated Fe(II), total dissolved iron(TDI), Mn(II), and total dissolved manganese(TDM) analysis system for the quality control of underground drinking water by reverse flow injection analysis and chemiluminescence detection(rFIA-CL), The method is based on the measurement of the metal-catalyzed light emission from luminol oxidation by potassium periodate. The typical signal is a narrow peak, in which the height is proportional to light emitted and hence to the concentration of metal ions. The detection limits were 3 x 10(-6) mu g ml(-1) for Fe(II) and the linear range extents up to 1.0 x 10(-4) and 5 x 10(-6) mu g ml(-1) for Mn(II) cover a linear range to 1.0 x 10(-4) mu g ml(-1). This method was used for automated in-situ monitoring of total dissolved iron and total dissolved in underground water during water treatment. (C) 1997 Elsevier Science B.V.

Consensus scoring for enriching near-native structures from protein-protein docking decoys

The identification of near native protein-protein complexes among a set of decoys remains highly challenging. A stategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near-native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near-native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu.

Refining near-native protein-protein docking decoys by local resampling and energy minimization

How to refine a near-native structure to make it closer to its native conformation is an unsolved problem in protein-structure and protein-protein complex-structure prediction. In this article, we first test several scoring functions for selecting locally resampled near-native protein-protein docking conformations and then propose a computationally efficient protocol for structure refinement via local resampling and energy minimization. The proposed method employs a statistical energy function based on a Distance-scaled Ideal-gas REference state (DFIRE) as an initial filter and an empirical energy function EMPIRE (EMpirical Protein-InteRaction Energy) for optimization and re-ranking. Significant improvement of final top-1 ranked structures over initial near-native structures is observed in the ZDOCK 2.3 decoy set for Benchmark 1.0 (74% whose global rmsd reduced by 0.5 angstrom or more and only 7% increased by 0.5 angstrom or more). Less significant improvement is observed for Benchmark 2.0 (38% versus 33%). Possible reasons are discussed.