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81.
P.V. Pogodin A.A. Lagunin D.A. Filimonov M.C. Nicklaus V.V. Poroikov 《SAR and QSAR in environmental research》2019,30(10):759-773
ABSTRACTExisting data on structures and biological activities are limited and distributed unevenly across distinct molecular targets and chemical compounds. The question arises if these data represent an unbiased sample of the general population of chemical-biological interactions. To answer this question, we analyzed ChEMBL data for 87,583 molecules tested against 919 protein targets using supervised and unsupervised approaches. Hierarchical clustering of the Murcko frameworks generated using Chemistry Development Toolkit showed that the available data form a big diffuse cloud without apparent structure. In contrast hereto, PASS-based classifiers allowed prediction whether the compound had been tested against the particular molecular target, despite whether it was active or not. Thus, one may conclude that the selection of chemical compounds for testing against specific targets is biased, probably due to the influence of prior knowledge. We assessed the possibility to improve (Q)SAR predictions using this fact: PASS prediction of the interaction with the particular target for compounds predicted as tested against the target has significantly higher accuracy than for those predicted as untested (average ROC AUC are about 0.87 and 0.75, respectively). Thus, considering the existing bias in the data of the training set may increase the performance of virtual screening. 相似文献
82.
Arsenidostannates with [SnAs] Nets Isostructural to Grey Arsenic: Synthesis and Crystal Structure of Na[Sn2As2], Na0.3Ca0.7[Sn2As2], Na0.4Sr0.6[Sn2As2], Na0.6Ba0.4[Sn2As2], and K0.3Sr0.7[Sn2As2] The metallic lustrous compounds Na[Sn2As2], Na0.3Ca0.7[Sn2As2], Na0.4Sr0.6[Sn2As2], Na0.6Ba0.4[Sn2As2] and K0.3Sr0.7[Sn2As2] were prepared from melts of mixtures of the elements. The compounds crystallize in the trigonal system (space group R3 m, No. 166, Z = 3) with lattice constants see in “Inhaltsübersicht”. The structures are isotypic to Sr[Sn2As2] containing puckered [SnAs] nets which are stacked with a sequence of six layers. The E(I)/E(II) atoms are located between each second [SnAs] layer in trigonal antiprismatic interstices formed by As atoms. In the resulting [Sn2As2] double layers the ∞2[SnAs] nets are stacked in such a way that additional Sn—Sn contacts arise. 相似文献
83.
84.
《Arabian Journal of Chemistry》2022,15(7):103933
In this study, a fingerprint-activity relationship modeling between chemical fingerprints and antirheumatic activity was established, and multivariate statistical analysis was used to evaluate the quality of Taxilli Herba (TH) from different hosts. Characteristic fingerprints of 20 batches of TH samples were generated by high-performance liquid chromatography coupled with triple quadrupole-time of flight tandem mass spectrometry (HPLC-Triple TOF-MS/MS), and the similarity analysis was calculated based on thirteen common characteristic peaks by hierarchical clustering analysis (HCA). Subsequently, nine efficacy markers were discovered by combining fingerprints and antirheumatic activity through grey correlation analysis (GCA) and bivariate correlation analysis (BCA). Meanwhile, the content of 5 constituents in 9 markers was determined by high-performance liquid chromatography coupled with triple quadrupole-linear ion trap tandem mass spectrometry (HPLC-QTRAP-MS/MS). The comprehensive quality of TH was assessed using multivariate statistical analysis, including principal components analysis (PCA) and technique for order preference by similarity to ideal solution (TOPSIS). The results showed that a high dose of TH extract could markedly ameliorate arthritis damage compared to other doses, with flavonoids playing an important role in the antirheumatic activity. The comprehensive quality of samples from Morus alba L. (SS) was superior to those from Liquidambar formosana Hance (FXS). The present study will demonstrate the markers associated with efficacy, and provide an applicable strategy for more comprehensive quality control and evaluation of TH. 相似文献
85.
Densification of boron carbide during sintering may be improved by a two-stage process, namely heating to 2000°C under vacuum and sintering at 2190°C under argon. This sintering regime allows achieving a relative density of the ceramic bodies fabricated from a fine powder higher than 95%. The nitrogen treatment of the boron carbide phase at 1900°C leads to the formation of the BN phase and precipitation of graphite. Vacuum treatment of these samples at 2000°C leads to decomposition of the boron nitride phase. The liberated free boron may again react with graphite to form in situ boron carbide particles. The experimental investigations of the sintering behavior of the boron carbide phase under various atmospheres supported the thermodynamic predictions regarding the phase transformation. No evidence, however, was found for enhanced sintering under a nitrogen atmosphere. 相似文献
86.
87.
C. I. J. M. Stuart 《Foundations of Physics Letters》1991,4(5):479-492
Aprediction puzzle leads to a form ofnecessary realism which forces the rejection of a central tenet of the Copenhagen interpretation. This leads to reconsidering conceptual difficulties related to Bell's locality premise. It is shown that aparadox of elementary probability theory puts new light on Bell's assumption that causality and statistical independence are mutually incompatible.
Nemo dat quod non habet : No one can offer more than he has ability to give; in that spirit, this paper is dedicated to the memory of J.S. Bell. 相似文献
88.
We investigate the application of torsion angle molecular dynamics (TAMD) to augment conformational sampling of peptides and proteins. Interesting conformational changes in proteins mainly involve torsional degrees of freedom. Carrying out molecular dynamics in torsion space does not only explicitly sample the most relevant degrees of freedom, but also allows larger integration time steps with elimination of the bond and angle degrees of freedom. However, the covalent geometry needs to be fixed during internal coordinate dynamics, which can introduce severe distortions to the underlying potential surface in the extensively parameterized modern Cartesian-based protein force fields. A "projection" approach (Katritch et al. J Comput Chem 2003, 24, 254-265) is extended to construct an accurate internal coordinate force field (ICFF) from a source Cartesian force field. Torsion crossterm corrections constructed from local molecular fragments, together with softened van der Waals and electrostatic interactions, are used to recover the potential surface and incorporate implicit bond and angle flexibility. MD simulations of dipeptide models demonstrate that full flexibility in both the backbone phi/psi and side chain chi1 angles are virtually restored. The efficacy of TAMD in enhancing conformational sampling is then further examined by folding simulations of small peptides and refinement experiments of protein NMR structures. The results show that an increase of several fold in conformational sampling efficiency can be reliably achieved. The current study also reveals some complicated intrinsic properties of internal coordinate dynamics, beyond energy conservation, that can limit the maximum size of the integration time step and thus the achievable gain in sampling efficiency. 相似文献
89.
Summary We have investigated to which extent retention data, acquired on single capillary columns, can be used for predicting retention factors in a coupled column system. For this purpose we utilized a model mixture of 18 lipid components with widely different vapor pressures and polarities. The sample was chromatographed on two columns, SB-biphenyl-30 (70% methyl-30% biphenylpolysiloxane) and SB-cyanopropyl-50 (50% methyl-50% cyanopropylsiloxane). Experimental retention factors, acquired in coupled column systems with two columns connected in different order, were thus compared with values calculated from runs on each single column. The agreement between calculated and experimental values generally was better than 5% without any pressure drop correction.To study the possibility of predicting retention behavior in a wide pressure range from a limited number of experiments, we also investigated the relation between solute retention and mobile phase density. We found that all data could be fitted to second order equations, which gives the possibility to optimize the resolution with respect to pressure from a limited number of runs at different pressures. 相似文献
90.
Efforts to develop a database of quadratic force fields for organic molecules are described. The database is based on systematic ab initio calculations, scaled to reproduce the experimentally observed frequencies. The choice of the theoretical method, the basis sets, geometries, internal coordinates and the scaling procedure are discussed. A key point in the procedure is the automatic generation of the internal valence coordinates. This is also very advantageous for geometry optimization. The database should permit the prediction of vibrational frequencies for most organic molecules to 10–20 cm−1, together with semiquantitative intensities. The accuracy is sufficient to identify unknown compounds from a list of reasonable candidates. 相似文献