当前位置： SCI文献检索 > Journal of Chemical Information and Modeling期刊下所有文献 > Characterization of DNA primary sequences by a new similarity/diversity measure based on the partial ordering.

Characterization of DNA primary sequences by a new similarity/diversity measure based on the partial ordering.

Abstract：

:The similarity/diversity measures play a fundamental role in library searching, virtual screening, and quantitative structure-activity relationship/quantitative structure-property relationship modeling as well as in genomics and proteomics. In this paper, a new similarity/diversity measure is proposed as a new approach for the analysis of sequential data, where useful information can be also obtained by the ordering relationships between the sequence elements. This methodology can be applied for evaluating molecular similarity/diversity, using sets of sequential descriptors, and for evaluating the similarity between spectra, sensor arrays, and other sequential data such as DNA and protein sequences. The new proposed distance (weighted standardized Hasse distance) is evaluated between pairs of Hasse matrices derived from the classical partial-ordering rules. It can be naturally standardized, thus allowing the interpretation of these distances as absolute values (e.g., percentage) and deriving simple similarity and correlation indices. A simple example is taken to highlight the behavior of the new similarity/diversity measure on DNA sequences taken from the first exons of the beta-globins for eight different species. Sensitivity analysis has been also performed, showing the high capability of this measure to take into account small modifications of the DNA sequences. Finally, a comparison with results obtained from the literature is given, together with a comparison with matrix invariants derived from the Hasse matrix.

journal_name

J Chem Inf Model

journal_title

Journal of chemical information and modeling

authors

Todeschini R,Consonni V,Mauri A,Ballabio D

doi

10.1021/ci060099e

subject

Has Abstract

pub_date

2006-09-01 00:00:00

pages

1905-11

issue

5

eissn

1549-9596

issn

1549-960X

journal_volume

46

pub_type

杂志文章

相关文献

Journal of Chemical Information and Modeling文献大全
  • Ab Initio Investigation of CO2 Adsorption on 13-Atom 4d Clusters.

    abstract：:In this work, we report an ab initio investigation based on density functional theory calculations within van der Waals D3 corrections to investigate the adsorption properties and activation of CO2 on transition-metal (TM) 13-atom clusters (TM = Ru, Rh, Pd, Ag), which is a key step for the development of subnano catal...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.9b00792

    authors： Batista KEA,Ocampo-Restrepo VK,Soares MD,Quiles MG,Piotrowski MJ,Da Silva JLF

    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

  • Molecular Mechanism, Dynamics, and Energetics of Protein-Mediated Dinucleotide Flipping in a Mismatched DNA: A Computational Study of the RAD4-DNA Complex.

    abstract：:DNA damage alters genetic information and adversely affects gene expression pathways leading to various complex genetic disorders and cancers. DNA repair proteins recognize and rectify DNA damage and mismatches with high fidelity. A critical molecular event that occurs during most protein-mediated DNA repair processes...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.7b00636

    authors： Pitta K,Krishnan M

    更新日期：2018-03-26 00:00:00

  • Factors affecting d-block metal-ligand bond lengths: toward an automated library of molecular geometry for metal complexes.

    abstract：:Metal-ligand (M-L) bond lengths for a range of ligands (carboxylates, chlorides, pyridines, water, tertiary phosphines, and alkenes) and a variety of metals have been retrieved from the Cambridge Structural Database, CSD. Analysis of the factors which affect M-L bond lengths (for example, ligand coordination mode, oxi...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci0500785

    authors： Harris SE,Orpen AG,Bruno IJ,Taylor R

    更新日期：2005-11-01 00:00:00

  • Exploration of the accessible chemical space of acyclic alkanes.

    abstract：:Saturated acyclic alkanes show steric strain if they are highly branched and, in extreme cases, fall apart rapidly at room temperature. Consequently, attempts to count the number of isomeric forms for a given molecular formula that neglect this physical consideration will inevitably overestimate the size of the availa...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci700246b

    authors： Paton RS,Goodman JM

    更新日期：2007-11-01 00:00:00

  • Accurate Estimation of pKb Values for Amino Groups from Surface Electrostatic Potential (VS,min) Calculations: The Isoelectric Points of Amino Acids as a Case Study.

    abstract：:Theoretical calculation of equilibrium dissociation constants is a very computationally demanding and time-consuming process since it requires an extremely accurate computation of the solvation free energy changes for each of the species involved. By correlating the minimum surface electrostatic potential (VS,min) on ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.9b01173

    authors： Sandoval-Lira J,Mondragón-Solórzano G,Lugo-Fuentes LI,Barroso-Flores J

    更新日期：2020-03-23 00:00:00

  • Partitioning of pi-electrons in rings for Clar structures of benzenoid hydrocarbons.

    abstract：:Resonance structures of polycyclic aromatic hydrocarbons can be associated with numerical formulas by assigning pi-electrons of C=C double bonds to individual benzenoid rings. Each C=C double bond in a resonance structure assigns two pi-electrons to a ring in a fused-benzenoid system if it is not shared by adjacent ri...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci050196s

    authors： Randić M,Balaban AT

    更新日期：2006-01-01 00:00:00

  • PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories.

    abstract：:Development of coarse-grained (CG) molecular dynamics models is often a laborious process which commonly relies upon approximations to similar models, rather than systematic parametrization. PyCGTOOL automates much of the construction of CG models via calculation of both equilibrium values and force constants of inter...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.7b00096

    authors： Graham JA,Essex JW,Khalid S

    更新日期：2017-04-24 00:00:00

  • Probing fragment complementation by rigid-body docking: in silico reconstitution of calbindin D9k.

    abstract：:Fragment complementation is gaining an increasing impact as a nonperturbing method to probe noncovalent interactions within protein supersecondary structures. In this study, the fast Fourier transform rigid-body docking algorithm ZDOCK has been employed for in silico reconstitution of the calcium binding protein calbi...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci0501995

    authors： Dell'Orco D,Seeber M,De Benedetti PG,Fanelli F

    更新日期：2005-09-01 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

  • GDP Release from the Open Conformation of Gα Requires Allosteric Signaling from the Agonist-Bound Human β2 Adrenergic Receptor.

    abstract：:G-protein-coupled receptors (GPCRs) transmit signals into the cell in response to ligand binding at its extracellular domain, which is characterized by the coupling of agonist-induced receptor conformational change to guanine nucleotide (GDP) exchange with guanosine triphosphate on a heterotrimeric (αβγ) guanine nucle...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.0c00432

    authors： Kumar V,Hoag H,Sader S,Scorese N,Liu H,Wu C

    更新日期：2020-08-24 00:00:00

  • Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a.

    abstract：:Peptides that bind to ion channels have attracted much interest as potential lead molecules for the development of new drugs and insecticides. However, the structure determination of large peptide-channel complexes using experimental methods is challenging. Thus structural models are often derived from combining exper...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.5b00529

    authors： Deplazes E,Davies J,Bonvin AM,King GF,Mark AE

    更新日期：2016-01-25 00:00:00

  • Dynamics of noncovalent interactions in all-α and all-β class proteins: implications for the stability of amyloid aggregates.

    abstract：:A fully folded functional protein is stabilized by several noncovalent interactions. When a protein undergoes conformational motions, the existing noncovalent interactions may be maintained. They may also break or new interactions may be formed. Knowledge of the dynamical nature of the different types of noncovalent i...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci200302q

    authors： Jain A,Sankararamakrishnan R

    更新日期：2011-12-27 00:00:00

  • Molecular Oxygen Binding in the Mitochondrial Electron Transfer Flavoprotein.

    abstract：:Reactive oxygen species such as superoxide are potentially harmful byproducts of the aerobic metabolism in the inner mitochondrial membrane, and complexes I, II, III of the electron transport chain have been identified as primary sources. The mitochondrial fatty acid b-oxidation pathway may also play a yet uncharacter...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.9b00702

    authors： Husen P,Nielsen C,Martino CF,Solov'yov IA

    更新日期：2019-11-25 00:00:00

  • Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs.

    abstract：:Although there are several databases that contain data on many metabolites and reactions in biochemical pathways, there is still a big gap in the numbers between experimentally identified enzymes and metabolites. It is supposed that many catalytic enzyme genes are still unknown. Although there are previous studies tha...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.5b00216

    authors： Moriya Y,Yamada T,Okuda S,Nakagawa Z,Kotera M,Tokimatsu T,Kanehisa M,Goto S

    更新日期：2016-03-28 00:00:00

  • Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes.

    abstract：:We report here on long-time all-atomistic molecular dynamics simulations of functional supramolecular nanotubes composed by the self-assembly of peptide-drug amphiphiles (DAs). These DAs have been shown to possess an inherently high drug loading of the hydrophobic anticancer drug camptothecin. We probe the self-assemb...

    journal_title：Journal of chemical information and modeling

    pub_type： 信件

    doi：10.1021/acs.jcim.8b00193

    authors： Kang M,Chakraborty K,Loverde SM

    更新日期：2018-06-25 00:00:00

  • Novel inhibitors of human histone deacetylase (HDAC) identified by QSAR modeling of known inhibitors, virtual screening, and experimental validation.

    abstract：:Inhibitors of histone deacetylases (HDACIs) have emerged as a new class of drugs for the treatment of human cancers and other diseases because of their effects on cell growth, differentiation, and apoptosis. In this study we have developed several quantitative structure-activity relationship (QSAR) models for 59 chemi...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci800366f

    authors： Tang H,Wang XS,Huang XP,Roth BL,Butler KV,Kozikowski AP,Jung M,Tropsha A

    更新日期：2009-02-01 00:00:00

  • The normal-mode entropy in the MM/GBSA method: effect of system truncation, buffer region, and dielectric constant.

    abstract：:We have performed a systematic study of the entropy term in the MM/GBSA (molecular mechanics combined with generalized Born and surface-area solvation) approach to calculate ligand-binding affinities. The entropies are calculated by a normal-mode analysis of harmonic frequencies from minimized snapshots of molecular d...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci3001919

    authors： Genheden S,Kuhn O,Mikulskis P,Hoffmann D,Ryde U

    更新日期：2012-08-27 00:00:00

  • iUmami-SCM: A Novel Sequence-Based Predictor for Prediction and Analysis of Umami Peptides Using a Scoring Card Method with Propensity Scores of Dipeptides.

    abstract：:Umami or the taste of monosodium glutamate represents one of the major attractive taste modalities in humans. Therefore, knowledge about biophysical and biochemical properties of the umami taste is important for both scientific research and the food industry. Experimental approaches for predicting umami peptides are l...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.0c00707

    authors： Charoenkwan P,Yana J,Nantasenamat C,Hasan MM,Shoombuatong W

    更新日期：2020-12-28 00:00:00

  • Development of an informatics platform for therapeutic protein and peptide analytics.

    abstract：:The momentum gained by research on biologics has not been met yet with equal thrust on the informatics side. There is a noticeable lack of software for data management that empowers the bench scientists working on the development of biologic therapeutics. SARvision|Biologics is a tool to analyze data associated with b...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci400333x

    authors： Hansen MR,Villar HO,Feyfant E

    更新日期：2013-10-28 00:00:00

  • Prediction of synthetic accessibility based on commercially available compound databases.

    abstract：:A compound's synthetic accessibility (SA) is an important aspect of drug design, since in some cases computer-designed compounds cannot be synthesized. There have been several reports on SA prediction, most of which have focused on the difficulties of synthetic reactions based on retro-synthesis analyses, reaction dat...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci500568d

    authors： Fukunishi Y,Kurosawa T,Mikami Y,Nakamura H

    更新日期：2014-12-22 00:00:00

  • Toward high throughput 3D virtual screening using spherical harmonic surface representations.

    abstract：:Searching chemical databases for possible drug leads is often one of the main activities conducted during the early stages of a drug development project. This article shows that spherical harmonic molecular shape representations provide a powerful way to search and cluster small-molecule databases rapidly and accurate...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci7001507

    authors： Mavridis L,Hudson BD,Ritchie DW

    更新日期：2007-09-01 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

  • Identification of novel potential antibiotics against Staphylococcus using structure-based drug screening targeting dihydrofolate reductase.

    abstract：:The emergence of multidrug-resistant Staphylococcus aureus (S. aureus) makes the treatment of infectious diseases in hospitals more difficult and increases the mortality of the patients. In this study, we attempted to identify novel potent antibiotic candidate compounds against S. aureus dihydrofolate reductase (saDHF...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci400686d

    authors： Kobayashi M,Kinjo T,Koseki Y,Bourne CR,Barrow WW,Aoki S

    更新日期：2014-04-28 00:00:00

  • Improved Chemical Structure-Activity Modeling Through Data Augmentation.

    abstract：:Extending the original training data with simulated unobserved data points has proven powerful to increase both the generalization ability of predictive models and their robustness against changes in the structure of data (e.g., systematic drifts in the response variable) in diverse areas such as the analysis of spect...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.5b00570

    authors： Cortes-Ciriano I,Bender A

    更新日期：2015-12-28 00:00:00

  • Multifingerprint based similarity searches for targeted class compound selection.

    abstract：:Molecular fingerprints are widely used for similarity-based virtual screening in drug discovery projects. In this paper we discuss the performance and the complementarity of nine two-dimensional fingerprints (Daylight, Unity, AlFi, Hologram, CATS, TRUST, Molprint 2D, ChemGPS, and ALOGP) in retrieving active molecules ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci0504723

    authors： Kogej T,Engkvist O,Blomberg N,Muresan S

    更新日期：2006-05-01 00:00:00

  • An integrated approach to ligand- and structure-based drug design: development and application to a series of serine protease inhibitors.

    abstract：:A novel approach was developed to rationally interface structure- and ligand-based drug design through the rescoring of docking poses and automated generation of molecular alignments for 3D quantitative structure-activity relationship investigations. The procedure was driven by a genetic algorithm optimizing the value...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci800015s

    authors： Nicolotti O,Miscioscia TF,Carotti A,Leonetti F,Carotti A

    更新日期：2008-06-01 00:00:00

  • Phosphorylation of Fibronectin Influences the Structural Stability of the Predicted Interchain Domain.

    abstract：:As a key player in cell adhesion, the glycoprotein fibronectin is involved in the complex mechanobiology of the extracellular matrix. Although the function of many modules in the fibronectin molecule has already been understood, the structure and biological relevance of the C-terminal cross-linked region (CTXL) still ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.9b00555

    authors： Kulke M,Uhrhan M,Geist N,Brüggemann D,Ohler B,Langel W,Köppen S

    更新日期：2019-10-28 00:00:00

  • Adaptive configuring of radial basis function network by hybrid particle swarm algorithm for QSAR studies of organic compounds.

    abstract：:The configuring of a radial basis function network (RBFN) consists of selecting the network parameters (centers and widths in RBF units and weights between the hidden and output layers) and network architecture. The issues of suboptimum and overfitting, however, often occur in RBFN configuring. This paper presented a ...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/ci600218d

    authors： Zhou YP,Jiang JH,Lin WQ,Zou HY,Wu HL,Shen GL,Yu RQ

    更新日期：2006-11-01 00:00:00

  • Perturbation-Theory and Machine Learning (PTML) Model for High-Throughput Screening of Parham Reactions: Experimental and Theoretical Studies.

    abstract：:Machine learning (ML) algorithms are gaining importance in the processing of chemical information and modeling of chemical reactivity problems. In this work, we have developed a perturbation-theory and machine learning (PTML) model combining perturbation theory (PT) and ML algorithms for predicting the yield of a give...

    journal_title：Journal of chemical information and modeling

    pub_type： 杂志文章

    doi：10.1021/acs.jcim.8b00286

    authors： Simón-Vidal L,García-Calvo O,Oteo U,Arrasate S,Lete E,Sotomayor N,González-Díaz H

    更新日期：2018-07-23 00:00:00