当前位置： SCI文献检索 > Journal of Chemical Information and Modeling期刊下所有文献 > Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics.

Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics.

Abstract：

:Large ring cyclodextrins have become increasingly important for drug delivery applications. In this work, we have performed replica-exchange molecular dynamics simulations using both implicit and explicit water solvation models to study the conformational diversity of iota-cyclodextrin containing 14 α-1,4 glycosidic linked d-glucopyranose units (CD14). The new quantifiable calculation methods are proposed to analyze the openness, bending, and twisted conformation of CD14 in terms of circularity, biplanar angle, and one-directional conformation (ODC). CD14 in GB implicit water model (Igb5) was found mostly in an opened conformation with average circularity of 0.39 ± 0.16 and a slight bend with average biplanar angle of 145.5 ± 16.0°. In contrast, CD14 in TIP3P explicit water solvation is significantly twisted with average circularity of 0.16 ± 0.10, while 29.1% are ODCs. In addition, classification of CD14 conformations using a Gaussian mixture model (GMM) shows that 85.0% of all CD14 in implicit water at 300 K correspond to the elliptical conformation, in contrast to 82.3% in twisted form in explicit water. GMM clustering also reveals minority conformations of CD14 such as the 8-shape, boat-form, and twisted conformations. This work provides fundamental insights into CD14 conformation, influence of solvation models, and also proposes new quantifiable analysis techniques for molecular conformation studies in the future.

journal_name

J Chem Inf Model

journal_title

Journal of chemical information and modeling

authors

Khuntawee W,Kunaseth M,Rungnim C,Intagorn S,Wolschann P,Kungwan N,Rungrotmongkol T,Hannongbua S

doi

10.1021/acs.jcim.6b00595

subject

Has Abstract

pub_date

2017-04-24 00:00:00

pages

778-786

issue

4

eissn

1549-9596

issn

1549-960X

journal_volume

57

pub_type

杂志文章

相关文献

Journal of Chemical Information and Modeling文献大全
  • QM/MM calculations in drug discovery: a useful method for studying binding phenomena?

    abstract：:Herein we investigate whether QM/MM could prove useful as a tool to study the often subtle binding phenomena found within pharmaceutical drug discovery programs. The goal of this investigation is to determine whether it is possible to employ high level QM/MM calculations to answer specific questions around a binding e...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci800419j

    authors： Gleeson MP,Gleeson D

    更新日期：2009-03-01 00:00:00

  • Combined Experimental and Molecular Simulation Study of Insulin-Chitosan Complexation Driven by Electrostatic Interactions.

    abstract：:Protein-polysaccharide complexes constructed via self-assembly methods are often used to develop novel biomaterials for a wide range of applications in biomedicine, food, and biotechnology. The objective of this work was to investigate theoretically and to demonstrate via constant-pH Monte Carlo simulations that the c...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.9b00814

    authors： Prudkin-Silva C,Pérez OE,Martínez KD,Barroso da Silva FL

    更新日期：2020-02-24 00:00:00

  • Rigidity Strengthening: A Mechanism for Protein-Ligand Binding.

    abstract：:Protein-ligand binding is essential to almost all life processes. The understanding of protein-ligand interactions is fundamentally important to rational drug and protein design. Based on large scale data sets, we show that protein rigidity strengthening or flexibility reduction is a mechanism in protein-ligand bindin...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.7b00226

    authors： Nguyen DD,Xiao T,Wang M,Wei GW

    更新日期：2017-07-24 00:00:00

  • Virtual drug screen schema based on multiview similarity integration and ranking aggregation.

    abstract：:The current drug virtual screen (VS) methods mainly include two categories. i.e., ligand/target structure-based virtual screen and that, utilizing protein-ligand interaction fingerprint information based on the large number of complex structures. Since the former one focuses on the one-side information while the later...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci200481c

    authors： Kang H,Sheng Z,Zhu R,Huang Q,Liu Q,Cao Z

    更新日期：2012-03-26 00:00:00

  • The molecular basis for the selectivity of tadalafil toward phosphodiesterase 5 and 6: a modeling study.

    abstract：:Great attention has been paid to the clinical significance of phosphodiesterase 5 (PDE5) inhibitors, such as sildenafil, tadalafil, and vardenafil widely used for erectile dysfunction. However, sildenafil causes side effects on visual functions since it shows similar potencies to inhibit PDE5 and PDE6, whereas tadalaf...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci400458z

    authors： Huang YY,Li Z,Cai YH,Feng LJ,Wu Y,Li X,Luo HB

    更新日期：2013-11-25 00:00:00

  • Diversity space and its application to library selection and design.

    abstract：:To promote more productive combinatorial endeavors, the Diversity Space methodology introduced here enables similarity comparisons at the library level. Particularly at an early screening stage, when little or no information is available regarding the pharmacophoric entities necessary for binding, it is more efficient...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci060066z

    authors： Fitzgerald SH,Sabat M,Geysen HM

    更新日期：2006-07-01 00:00:00

  • Facile Solutions to the Problems Associated with Chemical Information and Mathematical Symbolism While Using Machine Translation Tools.

    abstract：:Advances in computer-aided translation technology have made tremendous progress in accuracy in the past few years. Chemical Abstracts Service of the American Chemical Society summarizes scientific works from more than 50 languages and allows the users to search papers in nine selected languages. Currently, only the ab...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.0c00274

    authors： Wahab MF,Zulfiqar S,Sarwar MI,Lieberwirth I

    更新日期：2020-07-27 00:00:00

  • Random forest models to predict aqueous solubility.

    abstract：:Random Forest regression (RF), Partial-Least-Squares (PLS) regression, Support Vector Machines (SVM), and Artificial Neural Networks (ANN) were used to develop QSPR models for the prediction of aqueous solubility, based on experimental data for 988 organic molecules. The Random Forest regression model predicted aqueou...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci060164k

    authors： Palmer DS,O'Boyle NM,Glen RC,Mitchell JB

    更新日期：2007-01-01 00:00:00

  • Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets.

    abstract：:On the order of hundreds of absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) models have been described in the literature in the past decade which are more often than not inaccessible to anyone but their authors. Public accessibility is also an issue with computational models for bioactivity, a...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.5b00143

    authors： Clark AM,Dole K,Coulon-Spektor A,McNutt A,Grass G,Freundlich JS,Reynolds RC,Ekins S

    更新日期：2015-06-22 00:00:00

  • Ligand- and structure-based virtual screening for clathrodin-derived human voltage-gated sodium channel modulators.

    abstract：:Voltage-gated sodium channels (VGSC) are attractive targets for drug discovery because of the broad therapeutic potential of their modulators. On the basis of the structure of marine alkaloid clathrodin, we have recently discovered novel subtype-selective VGSC modulators I and II that were used as starting points for ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci400505e

    authors： Tomašić T,Hartzoulakis B,Zidar N,Chan F,Kirby RW,Madge DJ,Peigneur S,Tytgat J,Kikelj D

    更新日期：2013-12-23 00:00:00

  • Conformational determinants of the activity of antiproliferative factor glycopeptide.

    abstract：:The antiproliferative factor (APF) involved in interstitial cystitis is a glycosylated nonapeptide (TVPAAVVVA) containing a sialylated core 1 α-O-disaccharide linked to the N-terminal threonine. The chemical structure of APF was deduced using spectroscopic techniques and confirmed using total synthesis. The synthetic ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci400147s

    authors： Mallajosyula SS,Adams KM,Barchi JJ,MacKerell AD

    更新日期：2013-05-24 00:00:00

  • Critical Assessment of the Hildebrand and Hansen Solubility Parameters for Polymers.

    abstract：:Solubility parameter models are widely used to select suitable solvents/nonsolvents for polymers in a variety of processing and engineering applications. In this study, we focus on two well-established models, namely, the Hildebrand and Hansen solubility parameter models. Both models are built on the basis of the noti...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.9b00656

    authors： Venkatram S,Kim C,Chandrasekaran A,Ramprasad R

    更新日期：2019-10-28 00:00:00

  • Posetic quantitative superstructure/activity relationships (QSSARs) for chlorobenzenes.

    abstract：:As a result of the widespread industrial use of polychlorinated hydrocarbons, they have accumulated in nearly all types of environmental compartments, especially in aquatic systems. Particularly, chloroaromatics are among the most undesirable industrial effluents because of their persistence and toxicity. To predict c...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci0501342

    authors： Ivanciuc T,Ivanciuc O,Klein DJ

    更新日期：2005-07-01 00:00:00

  • Standardizing and simplifying analysis of peptide library data.

    abstract：:Peptide libraries allow researchers to quickly find hundreds of peptide sequences with a desired property. Currently, the large amount of data generated from peptide libraries is analyzed by hand, where researchers search for repeating patterns in the peptide sequences. Such patterns are called motifs. In this work, w...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci300484q

    authors： White AD,Keefe AJ,Nowinski AK,Shao Q,Caldwell K,Jiang S

    更新日期：2013-02-25 00:00:00

  • Elements of nucleotide specificity in the Trypanosoma brucei mitochondrial RNA editing enzyme RET2.

    abstract：:The causative agent of African sleeping sickness, Trypanosoma brucei , undergoes an unusual mitochondrial RNA editing process that is essential for its survival. RNA editing terminal uridylyl transferase 2 of T. brucei (TbRET2) is an indispensable component of the editosome machinery that performs this editing. TbR...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci3001327

    authors： Demir Ö,Amaro RE

    更新日期：2012-05-25 00:00:00

  • FlexAID: Revisiting Docking on Non-Native-Complex Structures.

    abstract：:Small-molecule protein docking is an essential tool in drug design and to understand molecular recognition. In the present work we introduce FlexAID, a small-molecule docking algorithm that accounts for target side-chain flexibility and utilizes a soft scoring function, i.e. one that is not highly dependent on specifi...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.5b00078

    authors： Gaudreault F,Najmanovich RJ

    更新日期：2015-07-27 00:00:00

  • PyPLIF HIPPOS: A Molecular Interaction Fingerprinting Tool for Docking Results of AutoDock Vina and PLANTS.

    abstract：:We describe here our tool named PyPLIF HIPPOS, which was newly developed to analyze the docking results of AutoDock Vina and PLANTS. Its predecessor, PyPLIF (https://github.com/radifar/pyplif), is a molecular interaction fingerprinting tool for the docking results of PLANTS, exclusively. Unlike its predecessor, PyPLIF...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.0c00305

    authors： Istyastono EP,Radifar M,Yuniarti N,Prasasty VD,Mungkasi S

    更新日期：2020-08-24 00:00:00

  • COSMOsar3D: molecular field analysis based on local COSMO σ-profiles.

    abstract：:The COSMO surface polarization charge density σ resulting from quantum chemical calculations combined with a virtual conductor embedding has been widely proven to be a very suitable descriptor for the quantification of interactions of molecules in liquids. In a preceding paper, grid-based local histograms of σ have be...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci300231t

    authors： Klamt A,Thormann M,Wichmann K,Tosco P

    更新日期：2012-08-27 00:00:00

  • Database of Nuclear Independent Chemical Shifts (NICS) versus NICSZZ of Polycyclic Aromatic Hydrocarbons (PAHs).

    abstract：:In the present contribution, we have developed a database, called the FAR-database, where the acronym FAR stands for Fused Aromatic Rings, which presents the results of nuclear independent chemical shifts calculations, NICS(0), NICS(1), NICS(0)ZZ, and NICS(1)ZZ, of 660 neutral benzenoid-PAHs and cyclopenta-fused PAHs....

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.9b00909

    authors： Alvarez-Ramírez F,Ruiz-Morales Y

    更新日期：2020-02-24 00:00:00

  • Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results.

    abstract：:In this work, we present a systematical investigation of the influence of ligand protonation states, stereoisomers, and tautomers on results obtained with the two protein-ligand docking programs GOLD and PLANTS. These different states were generated with a fully automated tool, called SPORES (Structure PrOtonation and...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci800420z

    authors： ten Brink T,Exner TE

    更新日期：2009-06-01 00:00:00

  • Discovery of wild-type and Y181C mutant non-nucleoside HIV-1 reverse transcriptase inhibitors using virtual screening with multiple protein structures.

    abstract：:To discover non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) that are effective against both wild-type (WT) virus and variants that encode the clinically troublesome Tyr181Cys (Y181C) RT mutation, virtual screening by docking was carried out using three RT structures and more than 2 million commercial...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci900068k

    authors： Nichols SE,Domaoal RA,Thakur VV,Tirado-Rives J,Anderson KS,Jorgensen WL

    更新日期：2009-05-01 00:00:00

  • Identifying promising compounds in drug discovery: genetic algorithms and some new statistical techniques.

    abstract：:Throughout the drug discovery process, discovery teams are compelled to use statistics for making decisions using data from a variety of inputs. For instance, teams are asked to prioritize compounds for subsequent stages of the drug discovery process, given results from multiple screens. To assist in the prioritizatio...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci600556v

    authors： Mandal A,Johnson K,Wu CF,Bornemeier D

    更新日期：2007-05-01 00:00:00

  • Property-Unmatched Decoys in Docking Benchmarks.

    abstract：:Enrichment of ligands versus property-matched decoys is widely used to test and optimize docking library screens. However, the unconstrained optimization of enrichment alone can mislead, leading to false confidence in prospective performance. This can arise by over-optimizing for enrichment against property-matched de...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.0c00598

    authors： Stein RM,Yang Y,Balius TE,O'Meara MJ,Lyu J,Young J,Tang K,Shoichet BK,Irwin JJ

    更新日期：2021-01-25 00:00:00

  • Relationships between Molecular Complexity, Biological Activity, and Structural Diversity.

    abstract：:Following the theoretical model by Hann et al. moderately complex structures are preferable lead compounds since they lead to specific binding events involving the complete ligand molecule. To make this concept usable in practice for library design, we studied several complexity measures on the biological activity of ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci0503558

    authors： Schuffenhauer A,Brown N,Selzer P,Ertl P,Jacoby E

    更新日期：2006-03-01 00:00:00

  • Virtual Screening with Generative Topographic Maps: How Many Maps Are Required?

    abstract：:Universal generative topographic maps (GTMs) provide two-dimensional representations of chemical space selected for their "polypharmacological competence", that is, the ability to simultaneously represent meaningful activity and property landscapes, associated with many distinct targets and properties. Several such GT...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.8b00650

    authors： Casciuc I,Zabolotna Y,Horvath D,Marcou G,Bajorath J,Varnek A

    更新日期：2019-01-28 00:00:00

  • Comparison of several molecular docking programs: pose prediction and virtual screening accuracy.

    abstract：:Molecular docking programs are widely used modeling tools for predicting ligand binding modes and structure based virtual screening. In this study, six molecular docking programs (DOCK, FlexX, GLIDE, ICM, PhDOCK, and Surflex) were evaluated using metrics intended to assess docking pose and virtual screening accuracy. ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci900056c

    authors： Cross JB,Thompson DC,Rai BK,Baber JC,Fan KY,Hu Y,Humblet C

    更新日期：2009-06-01 00:00:00

  • Benchmark data set for in silico prediction of Ames mutagenicity.

    abstract：:Up to now, publicly available data sets to build and evaluate Ames mutagenicity prediction tools have been very limited in terms of size and chemical space covered. In this report we describe a new unique public Ames mutagenicity data set comprising about 6500 nonconfidential compounds (available as SMILES strings and...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci900161g

    authors： Hansen K,Mika S,Schroeter T,Sutter A,ter Laak A,Steger-Hartmann T,Heinrich N,Müller KR

    更新日期：2009-09-01 00:00:00

  • Annotation of Allosteric Compounds to Enhance Bioactivity Modeling for Class A GPCRs.

    abstract：:Proteins often have both orthosteric and allosteric binding sites. Endogenous ligands, such as hormones and neurotransmitters, bind to the orthosteric site, while synthetic ligands may bind to orthosteric or allosteric sites, which has become a focal point in drug discovery. Usually, such allosteric modulators bind to...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.0c00695

    authors： Burggraaff L,van Veen A,Lam CC,van Vlijmen HWT,IJzerman AP,van Westen GJP

    更新日期：2020-10-26 00:00:00

  • Novel inhibitors of trihydroxynaphthalene reductase with antifungal activity identified by ligand-based and structure-based virtual screening.

    abstract：:Curvularia lunata is a dark pigmented fungus that is the causative agent of several diseases in plants and in both immunodeficient and immunocompetent patients. 1,8-Dihydroxynaphthalene-melanin is found in the cell wall of C. lunata and is believed to be the important virulence factor of dematiaceous fungi. Trihydroxy...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci2001499

    authors： Brunskole Svegelj M,Turk S,Brus B,Lanisnik Rizner T,Stojan J,Gobec S

    更新日期：2011-07-25 00:00:00

  • VMD Store-A VMD Plugin to Browse, Discover, and Install VMD Extensions.

    abstract：:Herein we present the VMD Store, an open-source VMD plugin that simplifies the way that users browse, discover, install, update, and uninstall extensions for the Visual Molecular Dynamics (VMD) software. The VMD Store obtains data about all the indexed VMD extensions hosted on GitHub and presents a one-click mechanism...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.9b00739

    authors： Fernandes HS,Sousa SF,Cerqueira NMFSA

    更新日期：2019-11-25 00:00:00