Abstract:
:The ONIOM2 (B3LYP/6-31G (d, p): PM3) and B3LYP/6-31G (d, p) methods were applied to investigate the interaction between STI-571 and abelson tyrosine kinase binding site. The complex of N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)- phenyl]-benzamide (part of STI-571) and related 16 amino acid residues were found at B3LYP/6-31G (d, p) level to have hydrogen bonds and pi....pi stacking interaction, their binding energy via HAF optimization was -20.4 kcal mol(-1). The results derived from this study agreed well with the reported observation.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Xiong YZ,Chen PYdoi
10.1007/s00894-008-0351-7subject
Has Abstractpub_date
2008-11-01 00:00:00pages
1083-6issue
11eissn
1610-2940issn
0948-5023journal_volume
14pub_type
杂志文章abstract::Four clusters of ZnO, O-Zn-SR (-SR = ligand) and doping ZnO structures (with Cr, Cu, Al atoms) were investigated using density functional theory at theB3LYP/Lanl2dz level. The characteristics of Zn(3)O(3) and Zn(4)O(4) structures, which are the units of experimental wurtzite and zinc blende structures, were found to b...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-010-0814-5
更新日期:2011-05-01 00:00:00
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journal_title:Journal of molecular modeling
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journal_title:Journal of molecular modeling
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更新日期:2016-05-01 00:00:00
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journal_title:Journal of molecular modeling
pub_type: 杂志文章
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更新日期:2019-01-31 00:00:00
abstract::G-Quadruplex and i-Motif-forming sequences in the promoter regions of several oncogenes show promise as targets for the regulation of oncogenes. In this study, molecular models were created for the c-MYC NHE-III(1) (nuclease hypersensitivity element III(1)) from two 39-base complementary sequences. The NHE modeled her...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
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更新日期:2008-02-01 00:00:00
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更新日期:2011-12-01 00:00:00
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journal_title:Journal of molecular modeling
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更新日期:2013-08-01 00:00:00
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abstract::Recently, the massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed. The present study aimed to determine whether the MP-CAFEE method is useful for drug discovery research. In the drug discovery process, it is important for computational chemists t...
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更新日期:2011-02-01 00:00:00
abstract::Tuberculosis still remains one of the most deadly infectious diseases. The emergence of drug resistant strains has fuelled the quest for novel drugs and drug targets for its successful treatment. Thymidine monophosphate kinase (TMPK) lies at the point where the salvage and de novo synthetic pathways meet in nucleotide...
journal_title:Journal of molecular modeling
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更新日期:2011-05-01 00:00:00
abstract::The binding properties of the protein-inhibitor complex of human immunodeficiency virus type 1 (HIV-1) protease with the inhibitor TMC-126 are investigated by combining computational alanine scanning (CAS) mutagenesis with binding free-energy decomposition (BFED). The calculated results demonstrate that the flap regio...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1205-2
更新日期:2012-05-01 00:00:00
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journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-008-0300-5
更新日期:2008-08-01 00:00:00
abstract::Modulation of γ-aminobutyric acid (GABA) levels has been required in various disorders. GABA itself cannot be directly introduced into central nervous system (CNS) because of the blood brain barrier; inhibition of GABA aminotransferase (GABA-AT), which degrades GABA in CNS, has been the target for the modulation of GA...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-020-04495-1
更新日期:2020-08-11 00:00:00
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journal_title:Journal of molecular modeling
pub_type: 杂志文章
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更新日期:2015-09-01 00:00:00
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journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1550-9
更新日期:2013-11-01 00:00:00
abstract::We examine a short way to reach an exceptional point that corresponds to a coalescence of two resonance energies. The application concerns the photodissociation of the Na2 molecule exposed to a laser field. In this case, the resonances can be correlated with the field-free vibrational states of the diatomic species. T...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1556-3
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abstract::Molecular-dynamics simulations have been used to study the diffusion of a short single model carbonic chain on the graphite (001) surface. The calculated diffusion coefficient (D) first increases, then decreases with increasing chain length (N). This abnormal behavior is similar to polymer lateral diffusion at the sol...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
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更新日期:2006-03-01 00:00:00
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journal_title:Journal of molecular modeling
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pub_type: 杂志文章
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更新日期:2012-06-01 00:00:00
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journal_title:Journal of molecular modeling
pub_type: 杂志文章
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更新日期:2013-04-01 00:00:00
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journal_title:Journal of molecular modeling
pub_type: 杂志文章
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更新日期:2017-12-20 00:00:00
abstract::The reaction mechanism of Ru-catalyzed cycloisomerization of 2-alkynylanilides to 3-substituted indole or 2-substituted indole was analyzed at the B3LYP level of density functional theory. The solvation effect of the system was also considered by SMD model. The calculation results show that the reaction system first f...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
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更新日期:2018-06-14 00:00:00
abstract::Physical and chemical adsorption of CO2 on ZnO surfaces were studied by means of two different implementations of periodic density functional theory. Adsorption energies were computed and compared to values in the literature. In particular, it was found that the calculated equilibrium structure and internuclear distan...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-012-1636-4
更新日期:2013-05-01 00:00:00
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journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-003-0151-z
更新日期:2003-10-01 00:00:00
abstract::Since the three-dimensional structure of the NMDA receptor has not been determined experimentally, indirect computer-assisted molecular modeling techniques appear to be of great usefulness in the characterization of the common pharmacophore of all NMDA receptor noncompetitive antagonists, despite their structural diff...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-001-0067-4
更新日期:2002-02-01 00:00:00
abstract::The nature and strength of intermolecular Se⋯N interaction between selenium-containing compounds HSeX (X = CH3, NH2, CF3, OCH3, CN, OH, NO2, Cl, F), and NH3 have been investigated at the MP2/aug-cc-pVDZ level. The Se⋯N interaction is found to be dependent on the substituent groups, which greatly affect the positive el...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
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更新日期:2016-01-01 00:00:00
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journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-013-1756-5
更新日期:2013-04-01 00:00:00
abstract::Tautomerism in monomers/dimers and association of 2,5-dihydroxy-1,8-naphthyridine was studied at the DFT level recently recommended for studies of non-covalent interactions. Studied dimers are stabilized by double and triple hydrogen-bonding. In some associates the intermolecular proton transfer may take place. Transi...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-011-1178-1
更新日期:2012-04-01 00:00:00
abstract::Vertical ionization energies (VIEs) of medazepam, nordazepam and their molecular subunits have been calculated using the electron propagator method in the P3/CEP-31G* approximation. Vertical electron affinities (VEAs) have been obtained with a ∆SCF procedure at the DFT-B3LYP/6-31+G* level of theory. Excellent correlat...
journal_title:Journal of molecular modeling
pub_type: 杂志文章
doi:10.1007/s00894-010-0723-7
更新日期:2011-02-01 00:00:00