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1.
Yu Liu Lei Zhao Wentao Li Dongyu Zhao Miao Song Yongliang Yang 《Journal of computational chemistry》2013,34(1):67-75
The accurate prediction of protein–ligand binding is of great importance for rational drug design. We present herein a novel docking algorithm called as FIPSDock, which implements a variant of the Fully Informed Particle Swarm (FIPS) optimization method and adopts the newly developed energy function of AutoDock 4.20 suite for solving flexible protein–ligand docking problems. The search ability and docking accuracy of FIPSDock were first evaluated by multiple cognate docking experiments. In a benchmarking test for 77 protein/ligand complex structures derived from GOLD benchmark set, FIPSDock has obtained a successful predicting rate of 93.5% and outperformed a few docking programs including particle swarm optimization (PSO)@AutoDock, SODOCK, AutoDock, DOCK, Glide, GOLD, FlexX, Surflex, and MolDock. More importantly, FIPSDock was evaluated against PSO@AutoDock, SODOCK, and AutoDock 4.20 suite by cross‐docking experiments of 74 protein–ligand complexes among eight protein targets (CDK2, ESR1, F2, MAPK14, MMP8, MMP13, PDE4B, and PDE5A) derived from Sutherland‐crossdock‐set. Remarkably, FIPSDock is superior to PSO@AutoDock, SODOCK, and AutoDock in seven out of eight cross‐docking experiments. The results reveal that FIPS algorithm might be more suitable than the conventional genetic algorithm‐based algorithms in dealing with highly flexible docking problems. © 2012 Wiley Periodicals, Inc. 相似文献
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James W. Cooley 《Mikrochimica acta》1987,93(1-6):33-45
The discovery of the fast Fourier transform (FFT) algorithm and the subsequent development of algorithmic and numerical methods based on it have had an enormous impact on the ability of computers to process digital representations of signals, or functions. At first, the FFT was regarded as entirely new. However, attention and wide publicity led to an unfolding of its pre-electronic computer history going back to Gauss. The present paper describes the author's own involvement and experience with the FFT algorithm.The author is grateful for permission from the Association for Computing Machinery to allow the present paper to bear some similarity with the paper,How the FFT Gained Acceptance, ref. [28] 相似文献
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We present a novel method to estimate the contributions of translational and rotational entropy to protein-ligand binding affinity. The method is based on estimates of the configurational integral through the sizes of clusters obtained from multiple docking positions. Cluster sizes are defined as the intervals of variation of center of ligand mass and Euler angles in the cluster. Then we suggest a method to consider the entropy of torsional motions. We validate the suggested methods on a set of 135 PDB protein-ligand complexes by comparing the averaged root-mean square deviations (RMSD) of the top-scored ligand docked positions, accounting and not accounting for entropy contributions, relative to the experimentally determined positions. We demonstrate that the method increases docking accuracy by 10-21% when used in conjunction with the AutoDock docking program, thus reducing the percent of incorrectly docked ligands by 1.4-fold to four-fold, so that in some cases the percent of ligands correctly docked to within an RMSD of 2 A is above 90%. We show that the suggested method to account for entropy of relative motions is identical to the method based on the Monte Carlo integration over intervals of variation of center of ligand mass and Euler angles in the cluster. 相似文献
5.
Norouzi Parviz Ganjali Mohammad Reza Qomi Mahnaz Nemati Kharat Ali Zamani Hassan Ali 《中国化学》2010,28(7):1133-1139
A continuous cyclic voltammetric study of letrozole at gold microelectrode was carried out. The drug in phosphate buffer (pH 2.0) is adsorbed at ?200 mV, giving rise to change in the current of well‐defined oxidation peak of gold in the flow injection system. The proposed detection method has some of advantages, the greatest of which are as follows: first, it is no more necessary to remove oxygen from the analyte solution and second, this is a very fast and appropriate technique for determination of the drug compound in a wide variety of chromatographic analysis methods. Signal‐to‐noise ratio has significantly increased by application of discrete Fast Fourier Transform (FFT) method, background subtraction and two‐dimensional integration of the electrode response over a selected potential range and time window. Also in this work some parameters such as sweep rate, eluent pH, and accumulation time and potential were optimized. The linear concentration range was of 1.0×10?7?1.0×10?10 mol/L (r=0.9975) with a limit of detection and quantitation 0.08 nmol/L and 0.15 nmol/L, respectively. The method has the requisite accuracy, sensitivity, precision and selectivity to assay letrozol in tablets. The influences of pH of eluent, accumulation potential, sweep rate, and accumulation time on the determination of the letrozol were considered. 相似文献
6.
《Journal of computational chemistry》2018,39(1):42-51
In this article, we present a new approach to expand the range of application of protein‐ligand docking methods in the prediction of the interaction of coordination complexes (i.e., metallodrugs, natural and artificial cofactors, etc.) with proteins. To do so, we assume that, from a pure computational point of view, hydrogen bond functions could be an adequate model for the coordination bonds as both share directionality and polarity aspects. In this model, docking of metalloligands can be performed without using any geometrical constraints or energy restraints. The hard work consists in generating the convenient atom types and scoring functions. To test this approach, we applied our model to 39 high‐quality X‐ray structures with transition and main group metal complexes bound via a unique coordination bond to a protein. This concept was implemented in the protein‐ligand docking program GOLD. The results are in very good agreement with the experimental structures: the percentage for which the RMSD of the simulated pose is smaller than the X‐ray spectra resolution is 92.3% and the mean value of RMSD is < 1.0 Å. Such results also show the viability of the method to predict metal complexes–proteins interactions when the X‐ray structure is not available. This work could be the first step for novel applicability of docking techniques in medicinal and bioinorganic chemistry and appears generalizable enough to be implemented in most protein‐ligand docking programs nowadays available. © 2017 Wiley Periodicals, Inc. 相似文献
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I. S. Moreira P. A. Fernandes M. J. Ramos 《International journal of quantum chemistry》2007,107(2):299-310
The definition and comprehension of the hot spots in an interface is a subject of primary interest for a variety of fields, including structure‐based drug design. Therefore, to achieve an alanine mutagenesis computational approach that is at the same time accurate and predictive, capable of reproducing the experimental mutagenesis values is a major challenge in the computational biochemistry field. Antibody/protein antigen complexes provide one of the greatest models to study protein–protein recognition process because they have three fundamentally features: specificity, high complementary association and a small epitope restricted to the diminutive complementary determining regions (CDR) region, while the remainder of the antibody is largely invariant. Thus, we apply a computational mutational methodological approach to the study of the antigen–antibody complex formed between the hen egg white lysozyme (HEL) and the antibody HyHEL‐10. A critical evaluation that focuses essentially on the limitations and advantages between different computational methods for hot spot determination, as well as between experimental and computational methodological approaches, is presented. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 相似文献
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An aminonaphthoquinone ligand, L, and its metal complexes of general formula [MLCl2] {M = Co(II), Ni(II), Cu(II) and Zn(II)} have been synthesized and characterized by analytical and spectral techniques. Tetrahedral geometry has been assigned to Ni(II) and Zn(II) complexes and square planar geometry to Co(II) and Cu(II) complexes on the basis of electronic spectral and magnetic susceptibility data. The binding of complexes with bovine serum albumin (BSA) is relatively stronger than that of free ligand and alters the conformation of the protein molecule. Interaction of these complexes with CT-DNA has been investigated using UV-Vis and fluorescence quenching experiments, which show that the complexes bind strongly to DNA through intercalative mode of binding (Kapp 105 M?1). Molecular docking studies reiterate the mode of binding of these compounds with DNA, proposed by spectral studies. The ligand and its complexes cleave plasmid DNA pUC18 to nicked (Form II) and linear (Form III) forms in the presence of H2O2 oxidant. The in vitro cytotoxicity screening shows that Cu(II) complex is more potent against MCF-7 cells and Zn(II) complex exhibits marked cytotoxicity against A-549 cells equal to that of cisplatin. Cell imaging studies suggested apoptosis mode of cell death in these two chosen cell lines. 相似文献
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Kazuhiro Ishida 《Journal of computational chemistry》2012,33(9):924-936
For calculating molecular integrals of systematic potentials, a three‐dimensional (3D) Fourier transform general formula can be derived, by the use of the Abel summation method. The present general formula contains all 3D Fourier transform formulas which are well known as Bethe–Salpeter formulas (Bethe and Salpeter, Handbuch der Physik, Bd. XXXV, 1957) as special cases. It is shown that, in several of the Bethe–Salpeter formulas, the integral does not converge in the meaning of the Riemann integral but converges in the meaning of a hyper function as the Schwartz distribution. For showing an effectiveness of the present general formula, the convergence condition of molecular integrals is derived generally for all of the present potentials. It is found that molecular integrals can be converged in the meaning of the Riemann integral for the present potentials, except for those for extra super singular potentials. It is also found that the convergence condition of molecular integrals over the Slater‐type orbitals is exactly the same as that of the corresponding integrals over the Gaussian‐type orbitals for the present systematic potentials. For showing more effectiveness, the molecular integral over the gauge‐including atomic orbitals is derived for the magnetic dipole‐same‐dipole interaction. © 2012 Wiley Periodicals, Inc. 相似文献
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P. Norouzi M. R. Ganjali A. S. Emami Meibodi B. Larijani 《Russian Journal of Electrochemistry》2008,44(9):1024-1030
Sotalol detection in tablets is achieved with the help of a newly developed, time-saving, and simple method, called fast Fourier
transform with continuous cyclic voltammetry (FFTCV). Noticeably, FFTCV illustrates two advantages, not being demonstrated
by earlier reports. First, there is no requirement for the oxygen removal from the test solution. In addition, the speed of
the method for determining any compound is high in a broad range of chromatographic methods. This research includes the observation
of effects of various parameters (influence of the pH of the eluent, accumulation potential, sweep rate, accumulation time)
on the sensitivity of the detection system. Finally, the technique was found to be linear for the concentration range of 3–14900
pg/ml (r = 0.998) with a limit of detection and quantitation of 0.95 pg/ml and 3 pg/ml, respectively.
Published in Russian in Elektrokhimiya, 2008, Vol. 44, No. 9, pp. 1103–1110.
The text was submitted by the authors in English. 相似文献
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《Journal of separation science》2018,41(7):1644-1650
A novel, simple, and inexpensive analytical technique based on flat sheet supported liquid membrane microextraction coupled with fast Fourier transform stripping cyclic voltammetry on a reduced graphene oxide carbon paste electrode was used for the extraction and online determination of diclofenac in whole blood. First, diclofenac was extracted from blood samples using a polytetrafluoroethylene membrane impregnated with 1‐octanol and then into an acceptor solution, subsequently it was oxidized on a carbon paste electrode modified with reduced graphene oxide nanosheets. The optimal values of the key parameters influencing the method were as follows: scan rate, 6 V/s; stripping potential, 200 mV; stripping time, 5 s; pH of the sample solution, 5; pH of the acceptor solution,7; and extraction time, 240 min. The calibration curves were plotted for the whole blood samples and the method was found to have a good linearity within the range of 1–25 μg/mL with a determination coefficient of 0.99. The limits of detection and quantification were 0.1 and 1.0 μg/mL, respectively. Using this coupled method, the extraction and determination were merged into one step. Accordingly, the speed of detection for sensitive determination of diclofenac in complex samples, such as blood, increased considerably. 相似文献
13.
Mohammad Reza Ganjali Parviz Norouzi Mashalah Zare 《Russian Journal of Electrochemistry》2008,44(10):1135-1143
An easy and fast Fourier transform continuous cyclic voltametric technique for monitoring of ultra trace amounts of metformin
in a flow-injection system has been introduced in this work. The potential waveform, consisting of the potential steps for
cleaning, stripping and potential ramp, was continuously applied on an Au disk microelectrode (12.5 μm in radius). The proposed
detection method has some of advantages, the greatest of which are as follows: first, it is no more necessary to remove oxygen
from the analyte solution and second, this is a very fast and appropriate technique for determination of the drug compound
in a wide variety of chromatographic analysis methods. The detection limit for metformin was 43 pg/ml. The relative standard
deviation (RSD) of the proposed technique at 5.0 × 10−7 M was 2.2% for 10 runs. The influences of pH of eluent, accumulation potential, sweep rate, and accumulation time on the
determination of the metformin were considered. The proposed method was applied to the determination of metformin in a pharmaceutical
preparation.
Published in Russian in Elektrokhimiya, 2008, Vol. 44, No. 10, pp. 1221–1230.
The text was submitted by the authors in English. 相似文献
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《Journal of computational chemistry》2018,39(11):621-636
According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the unbound ligand ensemble and a rigid receptor. Here, we use the fast Fourier transform (FFT) to efficiently evaluate BPMFs by calculating interaction energies when rigid ligand configurations from the unbound ensemble are discretely translated across rigid receptor conformations. Results for standard binding free energies between T4 lysozyme and 141 small organic molecules are in good agreement with previous alchemical calculations based on (1) a flexible complex ( for 24 systems) and (2) flexible ligand with multiple rigid receptor configurations ( for 141 systems). While the FFT is routinely used for molecular docking, to our knowledge this is the first time that the algorithm has been used for rigorous binding free energy calculations. © 2017 Wiley Periodicals, Inc. 相似文献
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We present a docking method that uses a scoring function for protein-ligand docking that is designed to maximize the docking success rate for low-resolution protein structures. We find that the resulting scoring function parameters are very different depending on whether they were optimized for high- or low-resolution protein structures. We show that this docking method can be successfully applied to predict the ligand-binding site of low-resolution structures. For a set of 25 protein-ligand complexes, in 76% of the cases, more than 50% of ligand-contacting residues are correctly predicted (using receptor crystal structures where the binding site is unspecified). Using decoys of the receptor structures having a 4 A RMSD from the native structure, for the same set of complexes, in 72% of the cases, we obtain at least one correctly predicted ligand-contacting residue. Furthermore, using an 81-protein-ligand set described by Jain, in 76 (93.8%) cases, the algorithm correctly predicts more than 50% of the ligand-contacting residues when native protein structures are used. Using 3 A RMSD from native decoys, in all but two cases (97.5%), the algorithm predicts at least one ligand-binding residue correctly. Finally, compared to the previously published Dolores method, for 298 protein-ligand pairs, the number of cases in which at least half of the specific contacts are correctly predicted is more than four times greater. 相似文献
17.
Design of Ligand Binding to an Engineered Protein Cavity Using Virtual Screening and Thermal Up-shift Evaluation 总被引:1,自引:0,他引:1
Machicado C López-Llano J Cuesta-López S Bueno M Sancho J 《Journal of computer-aided molecular design》2005,19(6):421-443
Summary Proteins could be used to carry and deliver small compounds. As a tool for designing ligand binding sites in protein cores,
a three-step virtual screening method is presented that has been optimised using existing data on T4 lysozyme complexes and
tested in a newly engineered cavity in flavodoxin. The method can pinpoint, in large databases, ligands of specific protein
cavities. In the first step, physico-chemical filters are used to screen the library and discard a majority of compounds.
In the second step, a flexible, fast docking procedure is used to score and select a smaller number of compounds as potential
binders. In the third step, a finer method is used to dock promising molecules of the hit list into the protein cavity, and
an optimised free energy function allows discarding the few false positives by calculating the affinity of the modelled complexes.
To demonstrate the portability of the method, several cavities have been designed and engineered in the flavodoxin from Anabaena PCC 7119, and the W66F/L44A double mutant has been selected as a suitable host protein. The NCI database has then been screened
for potential binders, and the binding to the engineered cavity of five promising compounds and three tentative non-binders
has been experimentally tested by thermal up-shift assays and spectroscopic titrations. The five tentative binders (some apolar
and some polar), unlike the three tentative non-binders, are shown to bind to the host mutant and, importantly, not to bind
to the wild type protein. The three-step virtual screening method developed can thus be used to identify ligands of buried
protein cavities. We anticipate that the method could also be used, in a reverse manner, to identify natural or engineerable
protein cavities for the hosting of ligands of interest. 相似文献
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Fault detection and diagnosis (FDD) have been major concerns in abnormal event management of chemical processes for decades. Frequency‐wise variations in chemical processes are not considered in most traditional methods, which affects the monitoring performance. An amplitude‐frequency images‐based convolutional neural network (ConvNet) is proposed for FDD in chemical processes. The fast Fourier transform (FFT) is first performed on data slice collected within a period to extract both amplitude‐wise dynamics and frequency‐wise variations, with the results in images. Then, the amplitude‐frequency images are fed into ConvNet for FDD. ConvNet is applied as a binary classifier, in which each classifier corresponds to only one fault. Thus, an expandable framework is provided to incorporate a new fault. The performance of the proposed amplitude‐frequency images‐based ConvNet in FDD is demonstrated in a numerical case and the Tennessee Eastman process. 相似文献
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Paper mulberry (Broussonetia papyrifera, syn. Morus papyrifera L.) is a Chinese traditional medicine and its low‐molecular‐weight extracts are reported to have antifungal activity. In this study, two proteins (PMAPI and PMAPII) with activity against Trichoderma viride were obtained from paper mulberry leaves with a fast protein liquid chromatography (FPLC) unit. The purification protocol employed (NH4)2SO4 precipitation, ion‐exchange chromatography and hydrophobic‐interaction chromatography on FPLC. Molecular masses were 18,798 Da for PMAPI, and 31,178 Da for PMAPII determined by Matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry. Peptide mapping fingerprint analysis showed that PMAPI has no peptides similar to PMAPII. N‐terminal amino acid sequencing revealed that PMAPI is a hevein‐like protein, and PMAPII is a class I chitinase. They both had a half‐maximal inhibitory concentration (IC50) of 0.1 µg/µL against T. viride. This is the first report of high‐molecular‐weight extracts with antifungal activity from paper mulberry. Copyright © 2011 John Wiley & Sons, Ltd. 相似文献
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Inrecentyears,oscillographictitrationhasbecomeanewareaofelectfotitrimetricanalysis.Yet,sincetherearesomeproblemsofreproducibility,sensitivityandresolvingpowerontheoscillogram,methodoftheoscillographicdeterminationformicroortracesubstancecannotbewellusedinactualanalysis..Inordertodevelopthemethod,theauthorshavestudiedthethreebasicproblems,exploredseveralnewoscillographicmethods,andimprovedsomeoldmethods.Asaresult,theoscillographicmethodhasexceededtherangeofthetitration,andhasgrowntobetheoscillo… 相似文献