当前位置： SCI文献检索 > JOURNAL OF MOLECULAR MODELING期刊下所有文献 > Multiple receptor conformation docking and dock pose clustering as tool for CoMFA and CoMSIA analysis - a case study on HIV-1 protease inhibitors.

Multiple receptor conformation docking and dock pose clustering as tool for CoMFA and CoMSIA analysis - a case study on HIV-1 protease inhibitors.

Abstract：

:Multiple receptors conformation docking (MRCD) and clustering of dock poses allows seamless incorporation of receptor binding conformation of the molecules on wide range of ligands with varied structural scaffold. The accuracy of the approach was tested on a set of 120 cyclic urea molecules having HIV-1 protease inhibitory activity using 12 high resolution X-ray crystal structures and one NMR resolved conformation of HIV-1 protease extracted from protein data bank. A cross validation was performed on 25 non-cyclic urea HIV-1 protease inhibitor having varied structures. The comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models were generated using 60 molecules in the training set by applying leave one out cross validation method, r (loo) (2) values of 0.598 and 0.674 for CoMFA and CoMSIA respectively and non-cross validated regression coefficient r(2) values of 0.983 and 0.985 were obtained for CoMFA and CoMSIA respectively. The predictive ability of these models was determined using a test set of 60 cyclic urea molecules that gave predictive correlation (r (pred) (2) ) of 0.684 and 0.64 respectively for CoMFA and CoMSIA indicating good internal predictive ability. Based on this information 25 non-cyclic urea molecules were taken as a test set to check the external predictive ability of these models. This gave remarkable out come with r (pred) (2) of 0.61 and 0.53 for CoMFA and CoMSIA respectively. The results invariably show that this method is useful for performing 3D QSAR analysis on molecules having different structural motifs.

journal_name

J Mol Model

journal_title

Journal of molecular modeling

authors

Sivan SK,Manga V

doi

10.1007/s00894-011-1048-x

subject

Has Abstract

pub_date

2012-02-01 00:00:00

pages

569-82

issue

2

eissn

1610-2940

issn

0948-5023

journal_volume

18

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR MODELING文献大全
  • Theoretical study of noncovalent interactions in XCN···YO2H (X = F, Cl, Br, I; Y = P, As, Sb) complexes.

    abstract：:Noncovalent interactions in XCN···YO2H (X = F, Cl, Br, I; Y = P, As, Sb) complexes were investigated using ab initio calculations at the MP2/aug-cc-pVDZ level of theory. There are four different configurations of these complexes, and the complexes are formed via hydrogen bonds, halogen bonds, π-hole interactions, or d...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3358-0

    authors： Zhao Q

    更新日期：2017-06-01 00:00:00

  • Receptor-guided 3D-QSAR approach for the discovery of c-kit tyrosine kinase inhibitors.

    abstract：:Studies of the the three-dimensional quantitative structure-activity relationships for ninety-five c-kit tyrosine kinase inhibitors were performed. Based on a co-crystallized compound (1 T46), known inhibitors were aligned with c-kit by induced-fit docking, and multiple training/test set splitting was performed to val...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1304-0

    authors： Almerico AM,Tutone M,Lauria A

    更新日期：2012-07-01 00:00:00

  • Rate constant calculations of the C2 + HCN → CCCN+H addition via the Master Equation.

    abstract：:The addition of C2 to HCN is of relevant interest in astrochemistry. We studied the pathways of this addition to produce CCCN and estimated its reaction rate using the Master Equation in the circumstellar environment. From the results of this study, it was possible to show that a different pathway in the Surface Poten...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3305-0

    authors： da Silva WB,Albernaz AF,Barreto PR,Correa E

    更新日期：2017-04-01 00:00:00

  • DFT study of sulfur derivatives of cumulenes and their protonated forms of interstellar interest and calculations of dissociation energies of protonated forms (SC(CH)C(n-2)S)(+) (n = 3-8).

    abstract：:A theoretical study of the sulfur cumulenes SCnS (n = 3-8), CnS ( n = 1-8) and of their protonated forms (SCnS)H(+) and (CnS)H(+) that might exist in the interstellar environment, has been carried out by means of the standard B3LYP/6-311G** method. The geometries and relative energies of singlet and triplet states acc...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2295-4

    authors： Benmensour MA,Djennane-Bousmaha S,Boucekkine A

    更新日期：2014-07-01 00:00:00

  • Chlorine gas reaction with ZnO wurtzoid nanocrystals as a function of temperature: a DFT study.

    abstract：:In the present work, we applied density functional theory and temperature-dependent Gibbs free energy calculations to wurtzoid structures to explain the sensitivity of ZnO nanocrystals towards chlorine molecules. In agreement with experimental findings, our results revealed that chlorine sensing under ambient conditio...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3309-9

    authors： Abdulsattar MA

    更新日期：2017-04-01 00:00:00

  • Water dimer isomers: interaction energies and electronic structure.

    abstract：:The energetic and electronic structure of various water dimer isomers has been explored through DFT methodology. Six different possible water dimers come in two broad categories, planar and non-planar. In each of the categories, three distinct topologies (i) linear, (ii) ring and (iii) bifurcated, have been obtained. ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-019-4274-2

    authors： Ghosh SR,Debnath B,Jana AD

    更新日期：2020-01-06 00:00:00

  • AM1 parameters for palladium and silver.

    abstract：:We report the parameterization of AM1 for the elements palladium and silver. The basis sets for both metals contain one set each of s-, p- and d-orbitals. AM1 parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Br, Zr, Mo, Pd, ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0940-0

    authors： Kayi H,Clark T

    更新日期：2011-10-01 00:00:00

  • Relationship between mutation of serine residue at 315th position in M. tuberculosis catalase-peroxidase enzyme and Isoniazid susceptibility: an in silico analysis.

    abstract：:Remarkable advances have been made in the drug therapy of tuberculosis. However much remains to be learned about the molecular and structural basis of drug resistance in Mycobacterium tuberculosis. It is known that, activation of Isoniazid (INH) is mediated by Mycobacterium tuberculosis catalase-peroxidase (MtBKatG) a...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0785-6

    authors： Purohit R,Rajendran V,Sethumadhavan R

    更新日期：2011-04-01 00:00:00

  • A theoretical investigation of one-dimensional lithium-bonded chain: enhanced first hyperpolarizability and little red-shift.

    abstract：:We present a theoretical investigation of the electric properties of two kinds of one-dimensional lithium bonded chains: (NC-Li)n and (NC-CC-Li)n (n = 1-8). The resulting (NC-Li)n and (NC-CC-Li)n were found to exhibit enhanced first hyperpolarizabilities (β 0) with increasing n, and a slight change in the absorption m...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2532-x

    authors： Ma F,Bai D,Xu H

    更新日期：2014-12-01 00:00:00

  • Molecular modeling study on chemically diverse series of cyclooxygenase-2 selective inhibitors: generation of predictive pharmacophore model using catalyst.

    abstract：:Cyclooxygenase (COX) enzymes catalyse the biosynthesis of prostaglandins and thromboxane from arachidonic acid (AA). We summarize in this paper, the development of pharmacophores of a dataset of inhibitors for COX-2 by using the Catalyst/Hypogen module using six chemically diverse series of compounds. Training set con...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-008-0350-8

    authors： Chopra M,Gupta R,Gupta S,Saluja D

    更新日期：2008-11-01 00:00:00

  • Computational studies on nitro derivatives of BN indole as high energetic material.

    abstract：:Nitrogen-rich heterocycles and their nitro derivatives are one of the important classes of energetic materials. In the present study, the computational methods have been applied to determine the thermodynamic and detonation properties of nitro derivatives of BN indole molecule. Structure optimization and electronic en...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-020-4337-4

    authors： Gupta S,Singh HJ

    更新日期：2020-03-24 00:00:00

  • Insights into the self-assembly steps of cyanuric acid toward rosette motifs: a DFT study.

    abstract：:The nature of non-covalent interactions in self-assembling systems is a topic that has aroused great attention in literature. In this field, the 1,3,5-triazinane-2,4,6-trione or cyanuric acid (CA) is one of the most widely used molecules to formulate self-assembled materials or monolayers. In the present work, a varie...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3428-3

    authors： Petelski AN,Peruchena NM,Pamies SC,Sosa GL

    更新日期：2017-08-14 00:00:00

  • One lithium atom binding with P-nitroaniline: lithium salts or lithium electrides?

    abstract：:Recently, both lithium (Li) salts and Li electrides formed by one Li atom interacting with ligand complexes, have been widely investigated. An interesting question emerges: is the configuration of one Li atom interacting with ligand complexes a Li salt or electride? In the present work, four configurations n-Li-PNA (n...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2560-6

    authors： Gao Y,Wu HQ,Sun SL,Xu HL,Su ZM

    更新日期：2015-02-01 00:00:00

  • Re-examining the procedure for simulating polymer Tg using molecular dynamics.

    abstract：:In this work, the poly(ethylene oxide) bulk as one example has been iteratively heated and cooled back using MD simulations to examine the effects of thermal history on the resulting Tg. It is demonstrated that, after the system is equilibrated once at the high temperatures, the simulated Tg does not exhibit a systema...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3439-0

    authors： Wu C

    更新日期：2017-08-22 00:00:00

  • The first intermediates in the bromination of bicyclo[3.3.1]nonylidenebicyclo[3.3.1]nonane, combination of experiments and theoretical results.

    abstract：:Bicyclo[3.3.1]nonylidenebicyclo[3.3.1]nonane (1) and adamantylideneadamantane (Ad=Ad) are two caged olefins with closely related structures at the double bond. Both compounds react instantaneously with Br2 in chlorinated hydrocarbon solvents to give mixtures of olefin-Br2 aggregates identified as the 1:1 pi-complex an...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-005-0038-2

    authors： Chiappe C,Pomelli CS,Lenoir D,Wattenbach C

    更新日期：2006-07-01 00:00:00

  • Density functional calculations of nickel, palladium and cadmium adsorption onto (10,0) single-walled carbon nanotube.

    abstract：:Adsorption of three heavy metals (Ni, Pd, Cd) onto (10,0) single-walled carbon nanotube (SWCNT) was investigated using density functional theory (DFT). Metals were adsorbed to both inside and outside of SWCNT and their structures and electronic properties [e.g., band structures and density of states (DOS)] were calcul...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-019-4062-z

    authors： Aghashiri A,Fotooh FK,Hashemian S

    更新日期：2019-06-10 00:00:00

  • The effect of cross linking density on the mechanical properties and structure of the epoxy polymers: molecular dynamics simulation.

    abstract：:Recently, great attention has been focused on using epoxy polymers in different fields such as aerospace, automotive, biotechnology, and electronics, owing to their superior properties. In this study, the classical molecular dynamics (MD) was used to simulate the cross linking of diglycidyl ether of bisphenol-A (DGEBA...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1906-9

    authors： Shokuhfar A,Arab B

    更新日期：2013-09-01 00:00:00

  • Identification and in silico analysis of a new group of double-histone fold-containing proteins.

    abstract：:The double-histone fold is a rare protein fold in which two consecutive regions characterized by the typical structure of histones assemble together, thus giving a histone pseudodimer. Previously, this fold was found in a few prokaryotic histones and in the regulatory region of guanine-nucleotide exchange factors of t...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-005-0008-8

    authors： Greco C,Sacco E,Vanoni M,De Gioia L

    更新日期：2005-12-01 00:00:00

  • Role of electronic kinetic energy and resultant gradient information in chemical reactivity.

    abstract：:The role of resultant gradient-information concept, reflecting the kinetic energy of electrons, in shaping the molecular electronic structure and reactivity preferences of open reactants is examined. This quantum-information descriptor combines contributions due to both the modulus (probability) and phase (current) co...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-019-4028-1

    authors： Nalewajski RF

    更新日期：2019-08-16 00:00:00

  • Pi-pi stacking tackled with density functional theory.

    abstract：:Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing pi-pi interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson-Crick pairs. Our main purpose...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-007-0239-y

    authors： Swart M,van der Wijst T,Fonseca Guerra C,Bickelhaupt FM

    更新日期：2007-12-01 00:00:00

  • DFT studies of the adsorption and dissociation of H₂O on the Al₁₃ cluster: origins of this reactivity and the mechanism for H₂ release.

    abstract：:A theoretical study of the chemisorption and dissociation pathways of water on the Al₁₃ cluster was performed using the hybrid density functional B3LYP method with the 6-311+G(d, p) basis set. The activation energies, reaction enthalpies, and Gibbs free energy of activation for the reaction were determined. Calculatio...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1730-7

    authors： Zhao JY,Zhao FQ,Gao HX,Ju XH

    更新日期：2013-04-01 00:00:00

  • Aluminum cluster for CO and O2 adsorption.

    abstract：:Low temperature oxidation of CO to CO2 is an important process for the environment. Similarly adsorption of CO from the releasing sources is also of major concern today. Whereas the potential of gold and silver clusters is well proven for the catalysis of the above mentioned reaction, the potential of aluminum (Al) cl...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-018-3869-3

    authors： Samanta B,Sengupta T,Pal S

    更新日期：2018-12-06 00:00:00

  • Spectroscopic and nonlinear optical properties of new chalcone fluorescent probes for bioimaging applications: a theoretical and experimental study.

    abstract：:In this study, the newly synthesized non-centrosymmetric, 4-dimethylamino-3'-isothiocyanatochalcone (PKA) compound was presented. This compound belongs to the chalcone group, and its main purpose is to be used in biomedical imaging as a fluorescence dye. For this reason, the linear and nonlinear properties in solvents...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-016-2990-4

    authors： Krawczyk P,Pietrzak M,Janek T,Jędrzejewska B,Cysewski P

    更新日期：2016-06-01 00:00:00

  • Effects of water content on the tetrahedral intermediate of chymotrypsin - trifluoromethylketone in polar and non-polar media: observations from molecular dynamics simulation.

    abstract：:The work uses MD simulation to study effects of five water contents (3 %, 10 %, 20 %, 50 %, 100 % v/v) on the tetrahedral intermediate of chymotrypsin - trifluoromethyl ketone in polar acetonitrile and non-polar hexane media. The water content induced changes in the structure of the intermediate, solvent distribution ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1807-y

    authors： Tian X,Jiang L,Yuan Y,Wang M,Guo Y,Zeng X,Li M,Pu X

    更新日期：2013-06-01 00:00:00

  • Effect of explicit water molecules on ligand-binding affinities calculated with the MM/GBSA approach.

    abstract：:We tested different approaches to including the effect of binding-site water molecules for ligand-binding affinities within the MM/GBSA approach (molecular mechanics combined with generalised Born and surface-area solvation). As a test case, we studied the binding of nine phenol analogues to ferritin. The effect of wa...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2273-x

    authors： Mikulskis P,Genheden S,Ryde U

    更新日期：2014-06-01 00:00:00

  • Computational and experimental studies on the triplet states of various N-substituted 4,5,6,7-tetrachlorophthalimides.

    abstract：:The triplet-triplet absorption spectra of three newly synthesized N-substituted 4,5,6,7-tetrachlorophthalimides (TCP) were measured experimentally and calculated with density functional theory. The heavy atom effect increases the intersystem crossing rate, and the transient triplet absorbance could be measured. Fluore...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2344-z

    authors： Kelterer AM,Mansha A,Iftikhar FJ,Zhang Y,Wang W,Xu JH,Grampp G

    更新日期：2014-07-01 00:00:00

  • Search for inhibitors of aminoacyl-tRNA synthases by virtual click chemistry.

    abstract：:The increase of multidrug-resistant strains of bacteria to known classes of antibiotics present a severe challenge for modern medicine. The most promising strategy to combat pathogenic bacteria is to discover new drug targets. In this regard, aminoacyl-tRNA synthetases are particularly well suited to develop novel dru...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-008-0421-x

    authors： Hoffmann M,Torchala M

    更新日期：2009-06-01 00:00:00

  • A comparative study on the B12N12, Al12N12, B12P12 and Al12P12 fullerene-like cages.

    abstract：:The stability, geometry and electronic structure of the title nanoclusters were compared by using density functional theory (DFT) calculations. Their electrical property analysis showed that the relative magnitude of the HOMO-LUMO gaps (eV) that are average values from the calculated results with five different DFT fu...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1286-y

    authors： Beheshtian J,Bagheri Z,Kamfiroozi M,Ahmadi A

    更新日期：2012-06-01 00:00:00

  • Insight into the molecular mechanism about lowered dihydrofolate binding affinity to dihydrofolate reductase-like 1 (DHFRL1).

    abstract：:Human dihydrofolate reductase-like 1 (DHFRL1) has been identified as a second human dihydrofolate reductase (DHFR) enzyme. Although DHFRL1 have high sequence homology with human DHFR, dihydrofolate (DHF) exhibits a lowered binding affinity to DHFRL1 and the corresponding molecular mechanism is still unknown. To addres...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-2018-2

    authors： Gao J,Cui W,Du Y,Ji M

    更新日期：2013-12-01 00:00:00

  • Electronic, ductile, phase transition and mechanical properties of Lu-monopnictides under high pressures.

    abstract：:The structural, elastic and electronic properties of lutatium-pnictides (LuN, LuP, LuAs, LuSb, and LuBi) were analyzed by using full-potential linearized augmented plane wave within generalized gradient approximation in the stable rock-salt structure (B1 phase) with space group Fm-3m and high-pressure CsCl structure (...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-2021-7

    authors： Gupta DC,Bhat IH

    更新日期：2013-12-01 00:00:00