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  • 1
    In: Journal of Computational Chemistry, Wiley, Vol. 43, No. 3 ( 2022-01-30), p. 160-169
    Abstract: AutoDock Vina (Vina) achieved a very high docking‐success rate, , but give a rather low correlation coefficient, , for binding affinity with respect to experiments. This low correlation can be an obstacle for ranking of ligand‐binding affinity, which is the main objective of docking simulations. In this context, we evaluated the dependence of Vina R coefficient upon its empirical parameters. is affected more by changing the gauss2 and rotation than other terms. The docking‐success rate is sensitive to the alterations of the gauss1, gauss2, repulsion, and hydrogen bond parameters. Based on our benchmarks, the parameter set1 has been suggested to be the most optimal. The testing study over 800 complexes indicated that the modified Vina provided higher correlation with experiment compared with obtained by the original Vina and by Vina version 1.2. Besides, the modified Vina can be also applied more widely, giving for 32/48 targets, compared with the default package, giving for 31/48 targets. In addition, validation calculations for 1036 complexes obtained from version 2019 of PDBbind refined structures showed that the set1 of parameters gave higher correlation coefficient ( ) than the default package ( ) and Vina version 1.2 ( ). The version of Vina with set1 of parameters can be downloaded at https://github.com/sontungngo/mvina . The outcomes would enhance the ranking of ligand‐binding affinity using Autodock Vina.
    Type of Medium: Online Resource
    ISSN: 0192-8651 , 1096-987X
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 1479181-X
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  • 2
    In: Diversity, MDPI AG, Vol. 15, No. 8 ( 2023-07-28), p. 894-
    Abstract: Dipterocarpus turbinatus C.F.Gaertn. is a valuable timber tree indigenous to the lowland tropical forests of southern and central Vietnam. It is in danger of extinction due to fragmented habitats and overexploitation. Therefore, assessing the genetic diversity and demographic history of this species is essential to providing a platform for conservation activities. Herein, we analyzed 281 D. turbinatus trees from 10 populations representing their natural distribution range in Vietnam using nine polymorphic microsatellites to provide valuable information for conservation activities. We detected genetic diversity within these populations (0.285 and 0.328 for observed and expected heterozygosity, respectively), as well as population genetic differentiation (a Wei and Cockerham value of 0.202 and a Hedrick value of 0.32). Clustering analysis based on different approaches revealed three genetic clusters which were significantly correlated to gene flow across the geographic distribution range of D. turbinatus in tropical evergreen forests. Approximate Bayesian computation suggested that the D. turbinatus populations had an evolutionary history consistent with divergence during the last glacial maximum. Based on our results, we recommend the in situ conservation of several populations with high genetic diversity, high allelic richness, or private alleles, and the gathering of the seeds of the remaining populations for ex situ conservation.
    Type of Medium: Online Resource
    ISSN: 1424-2818
    Language: English
    Publisher: MDPI AG
    Publication Date: 2023
    detail.hit.zdb_id: 2518137-3
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  • 3
    Online Resource
    Online Resource
    Publishing House for Science and Technology, Vietnam Academy of Science and Technology (Publications) ; 2019
    In:  TAP CHI SINH HOC Vol. 41, No. 1 ( 2019-03-28)
    In: TAP CHI SINH HOC, Publishing House for Science and Technology, Vietnam Academy of Science and Technology (Publications), Vol. 41, No. 1 ( 2019-03-28)
    Abstract: Dipterocarpus dyeri (Dipterocarpaceae) is widely distributed in lowland rainforests in southeastern Vietnam. Due to over- exploitation and habitat destruction in the 1980s and 1990s, this species is listed as threatened. Understanding the genetic variation and mating rate among D. dyeri population that occurs in forest patches is necessary to establish effectively conservation strategies for this species. To conserve the species in tropical forests, genetic diversity and mating rate were investigated using eight microsatellites (single sequence repeat, SSR) as markers. All of the eight loci were polymorphic. A total of 36 different alleles were observed across the loci screened. The SSR data indicated high genetic diversity (NA = 4.5; HO = 0.542 and HE = 0.667) and high inbreeding value, FIS= 0,182. The mating system parameters were determined using the mixed mating model and the results indicated high outcrossing rate (tm=0.81 and ts=0.675) and lowselfing rate (0.19). Difference of tm-ts value indicated that inbreeding contributed to selfing rate for this species in the Tan Phu tropical rain forest. The results reflected that D. dyeri habitat in this area has been restored and the number of individuals was high, about 500 individuals. However, seedlings were not found so far in this study. These results indicated the importance of conserving of the genetic resources of Dipterocarpus dyeri species in the Tan Phu rain forest. The conservation strategy should include an establishment of an ex-situ conservation site with new big population for this species from all genetic groups, which might improve its fitness under different environmental stresses.  
    Type of Medium: Online Resource
    ISSN: 0866-7160 , 0866-7160
    Language: Unknown
    Publisher: Publishing House for Science and Technology, Vietnam Academy of Science and Technology (Publications)
    Publication Date: 2019
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  • 4
    Online Resource
    Online Resource
    Publishing House for Science and Technology, Vietnam Academy of Science and Technology (Publications) ; 2018
    In:  Vietnam Journal of Biotechnology Vol. 16, No. 3 ( 2018-12-18), p. 431-437
    In: Vietnam Journal of Biotechnology, Publishing House for Science and Technology, Vietnam Academy of Science and Technology (Publications), Vol. 16, No. 3 ( 2018-12-18), p. 431-437
    Abstract: Human activities often lead to the disturbed and fragmented habitat and consequently threated species. Dipterocarpus dyeri (Dipterocarpaceae) is widely distributed in lowland rainforests in southeast Vietnam. Due to over- exploitation and habitat destruction in the 1980s and 1990s, the species is listed as threatened. Understanding the genetic variation and mating rate within D. dyeri population that occurs in forest patches is necessary to establish effectively conservation strategies for this species. To conserve the species in tropical forests, genetic diversity and mating rate were investigated on the basis of eight microsatellites (single sequence repeat, SSR). All of the eight loci were polymorphic. A total of 33 different alleles were observed across the screened loci. The SSR data indicated high genetic diversities (NA = 4.1; HO = 0.461 and HE = 0.543) and the inbreeding value was high (0.185). The mating system parameters were determined using the mixed mating model and indicated high outcrossing rates (tm = 0.884 and ts = 0.645). The differences of significant tm - ts value indicated that inbreeding contributed to selfing rate for this species in lowland tropical forests of Ma Da. This study also indicated the importance of conserving the genetic resources of Dipterocarpus dyeri species in Ma Da rainforests. Genetic conservation should derive from correlated outcrossing. The conservation strategy should be established an ex-situ conservation site with new big population for this species from all genetic groups, which might improve its fitness under different environmental stresses.
    Type of Medium: Online Resource
    ISSN: 1811-4989 , 1811-4989
    Language: Unknown
    Publisher: Publishing House for Science and Technology, Vietnam Academy of Science and Technology (Publications)
    Publication Date: 2018
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  • 5
    Online Resource
    Online Resource
    American Chemical Society (ACS) ; 2013
    In:  The Journal of Physical Chemistry A Vol. 117, No. 31 ( 2013-08-08), p. 6867-6882
    In: The Journal of Physical Chemistry A, American Chemical Society (ACS), Vol. 117, No. 31 ( 2013-08-08), p. 6867-6882
    Type of Medium: Online Resource
    ISSN: 1089-5639 , 1520-5215
    RVK:
    Language: English
    Publisher: American Chemical Society (ACS)
    Publication Date: 2013
    detail.hit.zdb_id: 2006031-2
    detail.hit.zdb_id: 1357795-5
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  • 6
    Online Resource
    Online Resource
    Elsevier BV ; 2014
    In:  Chemical Physics Letters Vol. 595-596 ( 2014-03), p. 272-276
    In: Chemical Physics Letters, Elsevier BV, Vol. 595-596 ( 2014-03), p. 272-276
    Type of Medium: Online Resource
    ISSN: 0009-2614
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2014
    detail.hit.zdb_id: 1466293-0
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  • 7
    In: Journal of Molecular Graphics and Modelling, Elsevier BV, Vol. 124 ( 2023-11), p. 108535-
    Type of Medium: Online Resource
    ISSN: 1093-3263
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 1491488-8
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  • 8
    In: The Journal of Chemical Physics, AIP Publishing, Vol. 136, No. 2 ( 2012-01-14)
    Abstract: The geometric structures of neutral and cationic SinLim0/+ clusters with n = 2–11 and m = 1, 2 are investigated using combined experimental and computational methods. The adiabatic ionization energy and vertical ionization energy (VIE) of SinLim clusters are determined using quantum chemical methods (B3LYP/6-311+G(d), G3B3, and CCSD(T)/aug-cc-pVxZ with x = D,T), whereas experimental values are derived from threshold photoionization experiments in the 4.68–6.24 eV range. Among the investigated cluster sizes, only Si6Li2, Si7Li, Si10Li, and Si11Li have ionization thresholds below 6.24 eV and could be measured accurately. The ionization threshold and VIE obtained from the experimental photoionization efficiency curves agree well with the computed values. The growth mechanism of the lithium doped silicon clusters follows some simple rules: (1) neutral singly doped SinLi clusters favor the Li atom addition on an edge or a face of the structure of the corresponding Sin− anion, while the cationic SinLi+ binds with one Si atom of the bare Sin cluster or adds on one of its edges, and (2) for doubly doped SinLi20/+ clusters, the neutrals have the shape of the Sin+1 counterparts with an additional Li atom added on an edge or a face of it, while the cations have both Li atoms added on edges or faces of the Sin− clusters.
    Type of Medium: Online Resource
    ISSN: 0021-9606 , 1089-7690
    Language: English
    Publisher: AIP Publishing
    Publication Date: 2012
    detail.hit.zdb_id: 3113-6
    detail.hit.zdb_id: 1473050-9
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  • 9
    Online Resource
    Online Resource
    The Royal Society ; 2021
    In:  Royal Society Open Science Vol. 8, No. 9 ( 2021-09), p. 210974-
    In: Royal Society Open Science, The Royal Society, Vol. 8, No. 9 ( 2021-09), p. 210974-
    Abstract: The winged-helix domain of the methyl methanesulfonate and ultraviolet-sensitive 81 ( w MUS81) is a potential cancer drug target. In this context, marine fungi compounds were indicated to be able to prevent w MUS81 structure via atomistic simulations. Eight compounds such as D197 ( Tryptoquivaline U ), D220 ( Epiremisporine B ), D67 ( Aspergiolide A ), D153 ( Preussomerin G ), D547 ( 12,13-dihydroxyfumitremorgin C ), D152 ( Preussomerin K ), D20 ( Marinopyrrole B ) and D559 ( Fumuquinazoline K ) were indicated that they are able to prevent the conformation of w MUS81 via forming a strong binding affinity to the enzyme via perturbation approach. The electrostatic interaction is the dominant factor in the binding process of ligands to w MUS81. The residues Trp55, Arg59, Leu62, His63 and Arg69 were found to frequently form non-bonded contacts and hydrogen bonds to inhibitors. Moreover, the influence of the ligand D197 , which formed the lowest binding free energy to w MUS81, on the structural change of enzyme was investigated using replica exchange molecular dynamics simulations. The obtained results indicated that D197 , which forms a strong binding affinity, can modify the structure of w MUS81. Overall, the marine compounds probably inhibit w MUS81 due to forming a strong binding affinity to the enzyme as well as altering the enzymic conformation.
    Type of Medium: Online Resource
    ISSN: 2054-5703
    Language: English
    Publisher: The Royal Society
    Publication Date: 2021
    detail.hit.zdb_id: 2787755-3
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  • 10
    Online Resource
    Online Resource
    Maxwell Scientific Publication Corp. ; 2013
    In:  Current Research Journal of Biological Sciences Vol. 5, No. 4 ( 2013-07-20), p. 141-148
    In: Current Research Journal of Biological Sciences, Maxwell Scientific Publication Corp., Vol. 5, No. 4 ( 2013-07-20), p. 141-148
    Type of Medium: Online Resource
    ISSN: 2041-076X , 2041-0778
    Language: Unknown
    Publisher: Maxwell Scientific Publication Corp.
    Publication Date: 2013
    detail.hit.zdb_id: 2546012-2
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