Search results for " set"
showing 10 items of 2095 documents
Protein structure prediction assisted with sparse NMR data in CASP13
2019
CASP13 has investigated the impact of sparse NMR data on the accuracy of protein structure prediction. NOESY and 15 N-1 H residual dipolar coupling data, typical of that obtained for 15 N,13 C-enriched, perdeuterated proteins up to about 40 kDa, were simulated for 11 CASP13 targets ranging in size from 80 to 326 residues. For several targets, two prediction groups generated models that are more accurate than those produced using baseline methods. Real NMR data collected for a de novo designed protein were also provided to predictors, including one data set in which only backbone resonance assignments were available. Some NMR-assisted prediction groups also did very well with these data. CAS…
3D-Chiral quadratic indices of the ‘molecular pseudograph’s atom adjacency matrix’ and their application to central chirality codification: classific…
2004
Quadratic indices of the 'molecular pseudograph's atom adjacency matrix' have been generalized to codify chemical structure information for chiral drugs. These 3D-chiral quadratic indices make use of a trigonometric 3D-chirality correction factor. These indices are nonsymmetric and reduced to classical (2D) descriptors when symmetry is not codified. By this reason, it is expected that they will be useful to predict symmetry-dependent properties. 3D-Chirality quadratic indices are real numbers and thus, can be easily calculated in TOMOCOMD-CARDD software. These descriptors circumvent the inability of conventional 2D quadratic indices (Molecules 2003, 8, 687-726. http://www.mdpi.org) and othe…
Atom-based Stochastic and non-Stochastic 3D-Chiral Bilinear Indices and their Applications to Central Chirality Codification
2006
Abstract Non-stochastic and stochastic 2D bilinear indices have been generalized to codify chemical structure information for chiral drugs, making use of a trigonometric 3D-chirality correction factor. In order to evaluate the effectiveness of this novel approach in drug design we have modeled the angiotensin-converting enzyme inhibitory activity of perindoprilate's σ-stereoisomers combinatorial library. Two linear discriminant analysis models, using non-stochastic and stochastic linear indices, were obtained. The models had shown an accuracy of 95.65% for the training set and 100% for the external prediction set. Next the prediction of the σ-receptor antagonists of chiral 3-(3-hydroxypheny…
A quantum-chemical study of the structure, vibrations and SiH bond properties of disilylamine, NH(SiH3)2.
2002
Quantum-chemical calculations at HF, MP2 and B3LYP levels with 6-31G* and 6-311G** basis sets are reported for disilylamine, NH(SiH3)2. The equilibrium structure is found to vary with both level and basis set, all but one of the structures exhibiting a small lack of planarity of the HNSi2 system. The barrier to inversion, however, is found to be very low, at most 38 cm(-1). Vibration frequencies and intensities are calculated. The frequencies are scaled, where possible, either using updated infrared data or with the aid of factors transferred from N(CH3)(SiH3)2. Unobserved frequencies due to the v(s)NSi2, deltaNSi2 and delta(perpendicular)NH modes are predicted near 610, 210 and 360 cm(-1),…
String kernels and high-quality data set for improved prediction of kinked helices in α-helical membrane proteins.
2011
The reasons for distortions from optimal α-helical geometry are widely unknown, but their influences on structural changes of proteins are significant. Hence, their prediction is a crucial problem in structural bioinformatics. For the particular case of kink prediction, we generated a data set of 132 membrane proteins containing 1014 manually labeled helices and examined the environment of kinks. Our sequence analysis confirms the great relevance of proline and reveals disproportionately high occurrences of glycine and serine at kink positions. The structural analysis shows significantly different solvent accessible surface area mean values for kinked and nonkinked helices. More important, …
Accurate Treatment of Large Supramolecular Complexes by Double-Hybrid Density Functionals Coupled with Nonlocal van der Waals Corrections.
2015
In this work, we present a thorough assessment of the performance of some representative double-hybrid density functionals (revPBE0-DH-NL and B2PLYP-NL) as well as their parent hybrid and GGA counterparts, in combination with the most modern version of the nonlocal (NL) van der Waals correction to describe very large weakly interacting molecular systems dominated by noncovalent interactions. Prior to the assessment, an accurate and homogeneous set of reference interaction energies was computed for the supramolecular complexes constituting the L7 and S12L data sets by using the novel, precise, and efficient DLPNO-CCSD(T) method at the complete basis set limit (CBS). The correction of the bas…
The prediction of molecular equilibrium structures by the standard electronic wave functions
1997
A systematic investigation has been carried out of the accuracy of molecular equilibrium structures of 19 small closed-shell molecules containing first-row atoms as predicted by the following standard electronic ab initio models: Hartree–Fock (HF) theory, Mo/ller–Plesset theory to second, third, and fourth orders (MP2, MP3, and MP4), coupled-cluster singles and doubles (CCSD) theory; CCSD theory with perturbational triples corrections [CCSD(T)], and the configuration-interaction singles and doubles (CISD) model. For all models, calculations were carried out using the correlation-consistent polarized valence double-zeta (cc-pVDZ) basis, the correlation-consistent polarized valence triple-zet…
A preliminary clinical trial using flowable glass-ionomer cement as a liner in proximal-ART restorations: the operator effect
2013
Objectives: This in vivo study was carried out to assess the influence of the operator experience on the survival rate of proximal-ART restorations using a two-layer technique to insert the glass-ionomer cement (GIC). Study Design: Forty five proximal cavities in primary molars were restored in a school setting according to the ART technique. The cavities were restored by two operators with Ketac Molar Easymix, and received a flowable layer of GIC prior to a second GIC layer with a regular consistency. The operators had different clinical experiences with ART (no experience or two years of experience), but both completed a one-week training to perform the restorations and the GIC mixing in …
Novel second-order nonlinear optical polymer materials containing indandione derivativatives as a chromophore
2006
Second order non linear optical (NLO) properties of sPMMA based host-guest systems containing eight dimethylaminobenzylidene -1, 3 - indandione (DMABI) related chromophores have been investigated by means of quantum chemical calculations and SHG experimental characterization. Ab initio calculations with basis set 6-31G were used for molecular geometry determination as well as in the calculations of molecular hyperpolarizability by FF approach. Influence of the chromophore concentration on the host-guest film NLO performance was obtained by SHG Maker fringe experiments. The highest value of d53233 =80 pm/V (frequency corrected value d033 =12 pm/V) at chromophore concentration 15 %wt have bee…
Real-Time Monocular Pose Estimation of 3D Objects Using Temporally Consistent Local Color Histograms
2017
We present a novel approach to 6DOF pose estimation and segmentation of rigid 3D objects using a single monocular RGB camera based on temporally consistent, local color histograms. We show that this approach outperforms previous methods in cases of cluttered backgrounds, heterogenous objects, and occlusions. The proposed histograms can be used as statistical object descriptors within a template matching strategy for pose recovery after temporary tracking loss e.g. caused by massive occlusion or if the object leaves the camera’s field of view. The descriptors can be trained online within a couple of seconds moving a handheld object in front of a camera. During the training stage, our approac…