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PubMedDate not supplied

Evaluation of a novel electronic eigenvalue (EEVA) molecular descriptor for QSAR/QSPR studies: validation using a benchmark steroid data set.

A novel electronic eigenvalue (EEVA) descriptor of molecular structure for use in the derivation of predictive QSAR/QSPR models is described. Like other spectroscopic QSAR/QSPR descriptors, EEVA is also invariant as to the alignment of the structures concerned. Its performance was tested with respect to the CBG (corticosteroid binding globulin) affinity of 31 benchmark steroids. It appeared that the electronic structure of the steroids, i.e., the "spectra" derived from molecular orbital energies, is directly related to the CBG binding affinities. The predictive ability of EEVA is compared to other QSAR approaches, and its performance is discussed in the context of the Hammett equation. The good performance of EEVA is an indication of the essential quantum mechanical nature of QSAR. The EEVA method is a supplement to conventional 3D QSAR methods, which employ fields or surface properties derived from Coulombic and van der Waals interactions.

Quantitative Structure-Activity Relationship↗

PubMedDate not supplied

Neighborhood behavior of in silico structural spaces with respect to in vitro activity spaces--a benchmark for neighborhood behavior assessment of different in silico similarity metrics.

In a previous work, we have introduced Neighborhood Behavior (NB) criteria for calculated molecular similarity metrics, based on the analysis of in vitro activity spaces that simultaneously monitor the responses of a compound with respect to an entire panel of biologically relevant receptors and enzymes. Now, these novel NB criteria will be used as a benchmark for the comparison of different in silico molecular similarity metrics, addressing the following topics: (1) the relative performance of 2D vs 3D descriptors, (2) the importance of the similarity scoring function for a given descriptor set, and (3) binary or Fuzzy Pharmacophore Fingerprints-can they capture the similarity of the spatial distribution of pharmacophoric groups despite different molecular connectivity? It was found that fuzzy pharmacophore descriptors (FBPA) displayed an optimal NB and, unlike their binary counterparts, were successful in evidencing pharmacophore pattern similarity independently of topological similarity. Topological FBPA, identical to the former except for the use of topological instead of 3D atom pair distances, display a somehow weaker, but significant NB. Metrics based on "classical" global 2D and 3D molecular descriptors and a Dice scoring function also performed well. The choice of the similarity scoring function is therefore as important as the choice of the appropriate molecular descriptors.

Journal Article↗

PubMedDate not supplied

FLUFF-BALL, a template-based grid-independent superposition and QSAR technique: validation using a benchmark steroid data set.

The Flexible Ligand Unified Force Field (FLUFF) is a molecular mechanistic superposition algorithm utilizing a template structure, on top of which the ligand(s) are superimposed. FLUFF enables a flexible semiautomatic superimposition in which the ligand and the template are allowed to seek the best common conformation, which can then be used to predict the biological activity by Boundless Adaptive Localized Ligand (BALL). In BALL, the similarity of the electrostatic and van der Waals volumes of the template and ligand is evaluated using the template-based coordinate system which makes the FLUFF-BALL invariant as to the rotations and translations of the global coordinate system. When tested using the CBG (corticosteroid binding globulin) affinities of 31 benchmark steroids, the FLUFF-BALL technique produced results comparable to standard 3D-QSAR methods. Supplementary test calculations were performed with five additional data sets. Due to its high level of automation and high throughput, the FLUFF-BALL is highly suitable for use in drug design and in scanning of large molecular libraries.

Algorithms↗

PubMedDate not supplied

Numerical performance and throughput benchmark for electronic structure calculations in PC-Linux systems with new architectures, updated compilers, and libraries.

A number of recently released numerical libraries including Automatically Tuned Linear Algebra Subroutines (ATLAS) library, Intel Math Kernel Library (MKL), GOTO numerical library, and AMD Core Math Library (ACML) for AMD Opteron processors, are linked against the executables of the Gaussian 98 electronic structure calculation package, which is compiled by updated versions of Fortran compilers such as Intel Fortran compiler (ifc/efc) 7.1 and PGI Fortran compiler (pgf77/pgf90) 5.0. The ifc 7.1 delivers about 3% of improvement on 32-bit machines compared to the former version 6.0. Performance improved from pgf77 3.3 to 5.0 is also around 3% when utilizing the original unmodified optimization options of the compiler enclosed in the software. Nevertheless, if extensive compiler tuning options are used, the speed can be further accelerated to about 25%. The performances of these fully optimized numerical libraries are similar. The double-precision floating-point (FP) instruction sets (SSE2) are also functional on AMD Opteron processors operated in 32-bit compilation, and Intel Fortran compiler has performed better optimization. Hardware-level tuning is able to improve memory bandwidth by adjusting the DRAM timing, and the efficiency in the CL2 mode is further accelerated by 2.6% compared to that of the CL2.5 mode. The FP throughput is measured by simultaneous execution of two identical copies of each of the test jobs. Resultant performance impact suggests that IA64 and AMD64 architectures are able to fulfill significantly higher throughput than the IA32, which is consistent with the SpecFPrate2000 benchmarks.

Journal Article↗

PubMedDate not supplied

GRID formalism for the comparative molecular surface analysis: application to the CoMFA benchmark steroids, azo dyes, and HEPT derivatives.

Shape analysis is a powerful tool in chemistry and drug design, and molecular surface defines shape in the molecular scale. In the current publication we presented a novel formalism for the comparative molecular surface analysis (s-CoMSA). The method enables both quantitative modeling of 3D-QSAR and finding possible pharmacophoric sites. The method provides very predictive models for the CBG activity of the benchmark steroid series, tinctorial properties of the heterocyclic azo dyes and anti-HIV activity of the HEPT series.

Anti-HIV Agents↗

PubMedDate not supplied

Benchmarking of linear and nonlinear approaches for quantitative structure-property relationship studies of metal complexation with ionophores.

A benchmark of several popular methods, Associative Neural Networks (ANN), Support Vector Machines (SVM), k Nearest Neighbors (kNN), Maximal Margin Linear Programming (MMLP), Radial Basis Function Neural Network (RBFNN), and Multiple Linear Regression (MLR), is reported for quantitative-structure property relationships (QSPR) of stability constants logK1 for the 1:1 (M:L) and logbeta2 for 1:2 complexes of metal cations Ag+ and Eu3+ with diverse sets of organic molecules in water at 298 K and ionic strength 0.1 M. The methods were tested on three types of descriptors: molecular descriptors including E-state values, counts of atoms determined for E-state atom types, and substructural molecular fragments (SMF). Comparison of the models was performed using a 5-fold external cross-validation procedure. Robust statistical tests (bootstrap and Kolmogorov-Smirnov statistics) were employed to evaluate the significance of calculated models. The Wilcoxon signed-rank test was used to compare the performance of methods. Individual structure-complexation property models obtained with nonlinear methods demonstrated a significantly better performance than the models built using multilinear regression analysis (MLRA). However, the averaging of several MLRA models based on SMF descriptors provided as good of a prediction as the most efficient nonlinear techniques. Support Vector Machines and Associative Neural Networks contributed in the largest number of significant models. Models based on fragments (SMF descriptors and E-state counts) had higher prediction ability than those based on E-state indices. The use of SMF descriptors and E-state counts provided similar results, whereas E-state indices lead to less significant models. The current study illustrates the difficulties of quantitative comparison of different methods: conclusions based only on one data set without appropriate statistical tests could be wrong.

Algorithms↗

PubMed1994

Compass: predicting biological activities from molecular surface properties. Performance comparisons on a steroid benchmark.

We describe a new method, Compass, for predicting the biological activities of molecules based on the activities and three-dimensional structures of other molecules. The method improves on previous techniques by representing only the surface of molecules, by incorporating a nonlinear statistical method, and by automatically choosing conformations and alignments of molecules. We use a benchmark problem of steroid binding affinity prediction to compare the performance of the method with that of two previous systems: CoMFA and a molecular similarity method. Compass predicts steroid affinities substantially more accurately than the others, which represent the state of the art. We present experiments showing that the improved performance depends on each of the technical innovations.

Algorithms↗

PubMed2006

Presentation of a structurally diverse and commercially available drug data set for correlation and benchmarking studies.

A multivariate analysis of drugs on the Swedish market was the basis for the selection of a small, physicochemically diverse set of 24 drug compounds. Factors such as structural diversity, commercial availability, price, and a suitable analytical technique for quantification were considered in the selection. Lipophilicity, pKa, solubility, and permeability across human Caco-2 cell monolayers were measured for the compiled data set. The results show that, by use of a physicochemically diverse data set, experimental responses over a wide range were obtained. The paper also shows how experimental difficulties due to the diversity of the data set can be overcome. We anticipate that this data set can serve as a benchmark set for validation of new experimental techniques or in silico models. It can also be used as a diverse starting data set for the development of new computational models.

Caco-2 Cells↗

PubMed2006

Benchmarking sets for molecular docking.

Ligand enrichment among top-ranking hits is a key metric of molecular docking. To avoid bias, decoys should resemble ligands physically, so that enrichment is not simply a separation of gross features, yet be chemically distinct from them, so that they are unlikely to be binders. We have assembled a directory of useful decoys (DUD), with 2950 ligands for 40 different targets. Every ligand has 36 decoy molecules that are physically similar but topologically distinct, leading to a database of 98,266 compounds. For most targets, enrichment was at least half a log better with uncorrected databases such as the MDDR than with DUD, evidence of bias in the former. These calculations also allowed 40x40 cross-docking, where the enrichments of each ligand set could be compared for all 40 targets, enabling a specificity metric for the docking screens. DUD is freely available online as a benchmarking set for docking at http://blaster.docking.org/dud/.

Adenosine Deaminase↗

PubMed2005

Benchmark database of barrier heights for heavy atom transfer, nucleophilic substitution, association, and unimolecular reactions and its use to test theoretical methods.

A benchmark database of forward and reverse barrier heights for 19 non-hydrogen-transfer reactions has been developed by using Weizmann 1 calculations, and 29 DFT methods and 6 ab initio wave-function theory (WFT) methods have been tested against the new database as well as against an older database for hydrogen atom transfer reactions. Among the tested hybrid DFT methods without kinetic energy density, MPW1K is the most accurate model for calculations of barrier heights. Among the tested hybrid meta DFT methods, BB1K and MPWB1K are the two most accurate models for the calculations of barrier heights. Overall, the results show that BB1K and MPWB1K are the two best DFT methods for calculating barrier heights, followed in order by MPW1K, MPWKCIS1K, B1B95, MPW1B95, BH and HLYP, B97-2, mPW1PW91, and B98. The popular B3LYP method has a mean unsigned error four times larger than that of BB1K. Of the methods tested, QCISD(T) is the best ab initio WFT method for barrier height calculations, and QCISD is second best, but QCISD is outperformed by the BB1K, MPWB1K, MPWKCIS1K, and MPW1K methods.

Journal Article↗

PubMed2006

Benchmark study of DFT functionals for late-transition-metal reactions.

The performance of a wide variety of DFT exchange-correlation functionals for a number of late-transition-metal reaction profiles has been considered. Benchmark ab-initio reference data for the prototype reactions Pd + H2, Pd + CH4, Pd + C2H6 (both C-C and C-H activation), and Pd + CH3Cl are presented, while ab-initio data of lesser quality were obtained for the catalytic hydrogenation of acetone and for the low-oxidation-state and high-oxidation-state mechanisms of the Heck reaction. "Kinetics" functionals such as mPW1K, PWB6K, BB1K, and BMK clearly perform more poorly for late-transition-metal reactions than for main-group reactions, as well as compared to general-purpose functionals. There is no single "best functional" for late-transition-metal reactions, but rather a cluster of several functionals (PBE0, B1B95, PW6B95, and TPSS25B95) that perform about equally well; if main-group thermochemical performance is additionally considered, then B1B95 and PW6B95 emerge as the best performers. TPSS25B95 and TPSS33B95 offer attractive performance compromises if weak interactions and main-group barrier heights, respectively, are also important. In the ab-initio calculations, basis set superposition errors (BSSE) can be greatly reduced by ensuring that the metal spd shell has sufficient radial flexibility in the high-exponent range. Optimal HF percentages in hybrid functionals depend on the class of systems considered, increasing from anions to neutrals to cations to main-group barrier heights; transition-metal barrier heights represent an intermediate situation. The use of meta-GGA correlation functionals appears to be quite beneficial.

Journal Article↗

PubMed1999

Evaluation of a novel molecular vibration-based descriptor (EVA) for QSAR studies: 2. Model validation using a benchmark steroid dataset.

The EVA molecular descriptor derived from calculated molecular vibrational frequencies is validated for use in QSAR studies. EVA provides a conformationally sensitive but, unlike 3D-QSAR methods such as CoMFA, superposition-free descriptor that has been shown to perform well with a wide range of datasets and biological endpoints. A detailed study is made using a benchmark steroid dataset with a training/test set division of structures. Intensive statistical validation tests are undertaken including various forms of crossvalidation and repeated random permutation testing. Latent variable score plots show that the distribution of structures in reduced dimensional space can be rationalized in terms of activity classes and that EVA is sensitive to structural inconsistencies. Together, the findings indicate that EVA is a statistically robust means of detecting structure-activity correlations with performance entirely comparable to that of analogous CoMFAs. The EVA descriptor is shown to be conformationally sensitive and as such can be considered to be a 3D descriptor but with the advantage over CoMFA that structural superposition is not required. EVA has the property that in certain situations the conformational sensitivity can be altered through the appropriate choice of the EVA sigma parameter.

Models, Molecular↗

PubMed2004

Environmental epidemiological study and estimation of benchmark dose for renal dysfunction in a cadmium-polluted area in China.

We have performed a study aimed at investigating the critical concentration of urinary cadmium (UCd) required for the development of renal dysfunction. We studied population groups (totally 790 persons) living in two cadmium exposed areas and one control area in China. UCd, was determined as an indicator of cadmium exposure and accumulation, while the concentrations of N-acetyl-beta-D-glucosaminidase (NAG), its iso-form B (NAG-B), beta2-microglobulin (B2M), retinol binding protein (RBP), and albumin (ALB) in urine were measured as indicators of the renal effects caused by cadmium. There was a significantly increased prevalence of hyperNAGuria, hyperNAG-Buria, hyperB2Muria, hyperRBPuria and hyperALBuria with increasing levels of Cd excretion in urine. We used the benchmark dose (BMD) procedure to estimate the critical concentration of urinary cadmium in this general population. The lower confidence limit of the BMD (LBMD-05) of urinary cadmium for a 5% level of risk above the background level was estimated for each of the renal effect indicators. The BMD-05/LBMD-05 were estimated to be 4.46/3.99, 6.70/5.87, 8.36/7.31, 7.98/6.98 and 15.06/12.18 microg/g creatinine for urinary NAG-B, NAG, B2M, RBP and ALB, respectively. Our findings suggest, based on the present study, that the Lower Confidence Limit of the Population Critical Concentration of UCd (LPCCUCd-05) of tubular dysfunction for 5% excess risk level above the background may be ca. 3-4 microg/g creatinine, and that cadmium concentration in urine should be kept below this level to prevent renal tubular damage. This report is the first to use the BMD method in this field and to define the concept of critical concentration in urine.

Acetylglucosaminidase↗

PubMed2003

Effectiveness of cognitive therapy for depression in a community mental health center: a benchmarking study.

The current study examined the feasibility and effectiveness of transporting an empirically supported treatment for depression, cognitive therapy (CT), to a community mental health center setting. CT was delivered to 192 adult outpatients with major depression, and a benchmarking strategy compared results with those of 2 randomized controlled trials (RCTs). The 3 samples were largely similar in terms of initial severity of depression, and CT was as effective in reducing depressive symptoms in the current sample as in the RCTs. More favorable outcome was associated with less severe initial depression, more therapy sessions, more years of education, and absence of a comorbid personality disorder. This study demonstrates that an empirically supported treatment can be transported effectively to a clinical setting.

Adult↗

PubMed2006

Quantification of antibody responses against multiple antigens of the two infectious forms of Vaccinia virus provides a benchmark for smallpox vaccination.

Smallpox was eradicated without an adequate understanding of how vaccination induced protection. In response to possible bioterrorism with smallpox, the UK government vaccinated approximately 300 health care workers with vaccinia virus (VACV) strain Lister. Antibody responses were analyzed using ELISA for multiple surface antigens of the extracellular enveloped virus (EEV) and the intracellular mature virus (IMV), plaque reduction neutralization and a fluorescence-based flow cytometric neutralization assay. Antibody depletion experiments showed that the EEV surface protein B5 is the only target responsible for EEV neutralization in vaccinated humans, whereas multiple IMV surface proteins, including A27 and H3, are targets for IMV-neutralizing antibodies. These data suggest that it would be unwise to exclude the B5 protein from a future smallpox vaccine. Repeated vaccination provided significantly higher B5-specific and thus EEV-neutralizing antibody responses. These data provide a benchmark against which new, safer smallpox vaccines and residual immunity can be compared.

Antibodies, Viral↗

PubMed2006

Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs.

MP2 and CCSD(T) complete basis set (CBS) limit interaction energies and geometries for more than 100 DNA base pairs, amino acid pairs and model complexes are for the first time presented together. Extrapolation to the CBS limit is done by using two-point extrapolation methods and different basis sets (aug-cc-pVDZ - aug-cc-pVTZ, aug-cc-pVTZ - aug-cc-pVQZ, cc-pVTZ - cc-pVQZ) are utilized. The CCSD(T) correction term, determined as a difference between CCSD(T) and MP2 interaction energies, is evaluated with smaller basis sets (6-31G** and cc-pVDZ). Two sets of complex geometries were used, optimized or experimental ones. The JSCH-2005 benchmark set, which is now available to the chemical community, can be used for testing lower-level computational methods. For the first screening the smaller training set (S22) containing 22 model complexes can be recommended. In this case larger basis sets were used for extrapolation to the CBS limit and also CCSD(T) and counterpoise-corrected MP2 optimized geometries were sometimes adopted.

Amino Acids↗

PubMed2002

Haemophilia care in the developing world: benchmarking for excellence.

Seventy-five percent of patients with haemophilia receive no or inadequate treatment, and often do not survive to adulthood. With efficient organization, the disorder is treatable and becomes part of normal life. In developing countries there is a large discrepancy in haemophilia care. Some have zero treatment levels, while others already have comprehensive care centres. This paper attempts to assess and standardize the levels of haemophilia care for developing countries, setting up benchmarks or guidelines for future development. Four major areas are emphasized: clinical care, laboratory, blood products and patient organization. For each country or community, development work begins after the assessment of competency level in each area. The next step is then to plan, organize, improve and move up to the next level. To become successful, a sound and realistic strategy should be employed, starting from the identification of key leaders and the recruitment of an expert team. To obtain recognition and support from health authorities, the haemophilia care programme should not limit itself to haemophilia care but should also include medical care for all bleeding disorders, including the improvement of blood banks, blood products, coagulation laboratories and other medical facilities. This would directly improve the overall medical care standard of the whole hospital. It is also important to emphasize the need for selfreliance, employing simple yet effective methodology, equipment and mechanical facilities. The effective coordination of World Federation of Hemophilia assistance and the host country's committed action will ensure success in the emerging trend of better haemophilia care in developing countries.

Blood Banks↗

PubMed2004

Ab initio study on the spectroscopy of CuCl2. I. Benchmark calculations on the X2Pig - 2Sigmag+ transition.

The modern theoretical predictions on the LambdaSSigma nature of the ground state of CuCl2 have led to different answers, depending on the type (DFT-based or ab initio) and the quality of the electronic correlation treatment; for this reason the X2Pig - 2Sigmag+ transition energy has been predicted to range from -1856 to +5887 cm(-1). The physical problem at hand lies in the difficulty of accurately describing the orientation of the 3d hole on the central Cu2+(3d9)/Cu+(3d94s1) ion (in the field of both chlorine ions), which implies the need of the most sophisticated nondynamic and dynamic electronic correlation treatments. We report here ab initio benchmark calculations using especially developed basis sets to study, at the CASSCF + CASPT2 and CASSCF + ACPF levels, the transition energy as well as the corresponding equilibrium geometries. The spin-orbit (SO) effects of both atoms were included in a second step through the effective Hamiltonian formalism, using the calibrated SO effective potentials developed by the Stuttgart group. Without SO at the CASSCF + ACPF level, the ground state is X2Pig but the vertical transition energy to the 2Sigmag+ is only 99 cm(-1) at 3.95 a.u. The inclusion of the SO effects leads to a Omega = 1/2 (59% 2Pig,41% 2Sigmag+) ground state, in contradiction with the Omega experimental value of 3/2. In a last step we show that the SO effects (and therefore the final Omega ordering) are critically dependent on the LambdaSSigma electronic energies, so that it is not impossible that the Omega ordering is actually changed. For theoreticians interest in this matter is not purely academic, since many properties of organometallic complexes are linked to such delicate physical effects.

Journal Article↗