Abstract:
:Identifying and predicting the structural characteristics of novel repeats throughout the genome can lend insight into biological function. Specific repeats are believed to have biological significance as a function of their distribution patterns. We have developed 'GenomeMark,' a computer program that detects and statistically analyzes candidate repeats. Specifically, 'GenomeMark' identifies the periodic distribution of unique words, calculating their chi2 and Z-score values. Using 'GenomeMark,' we identified novel sequence words present in tandem throughout genomes. We found that these sequences have remarkable spacer sequence distributions and many were genome specific, validating the genome signature theory. Further analysis confirmed that many of these sequences have a specific biological function. The program is available from the authors upon request and is freely available for non-commercial and academic entities.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Fadiel A,Eichenbaum KD,Hamza Adoi
10.1080/07391102.2006.10507071subject
Has Abstractpub_date
2006-02-01 00:00:00pages
457-64issue
4eissn
0739-1102issn
1538-0254pii
d=3024&c=4193&p=13245&do=detailjournal_volume
23pub_type
杂志文章abstract::The acute respiratory syndrome caused by the SARS-CoV-2, known as COVID-19, has been ruthlessly tormenting the world population for more than six months. However, so far no effective drug or vaccine against this plague have emerged yet, despite the huge effort in course by researchers and pharmaceutical companies worl...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1869096
更新日期:2021-01-08 00:00:00
abstract::Hydroxylation of proline or lysine residues in proteins is a common post-translational modification event, and such modifications are found in many physiological and pathological processes. Nonetheless, the exact molecular mechanism of hydroxylation remains under investigation. Because experimental identification of h...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2016.1163294
更新日期:2017-03-01 00:00:00
abstract::Haloxyfop was reported to exhibit inhibition effect targeting Mycobacterium tuberculosis and pathogenic parasites. To pave its way for drug development, more research is required to determine the affinities interacting with biological receptors in vivo. In this work, the interactions of Haloxyfop with two model transp...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1552624
更新日期:2019-10-01 00:00:00
abstract::The hexachlorocyclotriphosphaze compound (N3P3Cl6, HCCP) was reacted with excess (E)-(1-(4'-oxyphenyl)-3-(substituted-phenyl)prop-2-en-1-ones (2-11) to produce hexakis[(1-(4-oxyphenyl)-3-(substituted-phenyl)prop-2-en-1-one)]cyclotriphosphazenes (CP 2-11). The structures of products (CP 2-11) were confirmed using eleme...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1846621
更新日期:2020-11-19 00:00:00
abstract::Adenosine receptors (ARs) belong to family A of GPCRs that are involved in many diseases, including cerebral and cardiac ischemic diseases, immune and inflammatory disorders, etc. Thus, they represent important therapeutic targets to treat these conditions. Computational techniques such as molecular dynamics (MD) simu...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1564700
更新日期:2019-11-01 00:00:00
abstract::Communicated by Ramaswamy H. Sarma. ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 信件
doi:10.1080/07391102.2020.1844052
更新日期:2020-11-06 00:00:00
abstract::Raman spectroscopy has been used to study the eigenvectors and eigenvalues of the vibrational modes of crystalline cytidine at 295 K and high pressures by evaluating the logarithmic derivative of the vibrational frequency ω with respect to pressure P: [Formula: see text]. Crystalline samples of molecular materials hav...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2014.915763
更新日期:2015-01-01 00:00:00
abstract::Base sequence effects within double stranded RNA oligomers of A and Z conformations have been studied by molecular modeling using a methodological approach specifically adapted to nucleic acids. Calculations on symmetric oligomers having homonucleotide or dinucleotide repeating base sequences show that sequence change...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1989.10507778
更新日期:1989-10-01 00:00:00
abstract::Continuum finite element material models used for traumatic brain injury lack local injury parameters necessitating nanoscale mechanical injury mechanisms be incorporated. One such mechanism is membrane mechanoporation, which can occur during physical insults and can be devastating to cells, depending on the level of ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1453376
更新日期:2019-03-01 00:00:00
abstract::The problem that how many protein-coding genes there are in the genome of Aeropyrum pernix K1 has confused many scientists since the sequencing in 1999. In this paper, the protein-coding genes in A. pernix K1 are identified from the original and current NITE annotation by using the Aper_ORFs method. Consequently, 702 ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2009.10507256
更新日期:2009-02-01 00:00:00
abstract::Triplex and duplex formation of two deoxyribohexadecamers d-A-(G-A)-G (a) and d-C-(T-C)-T (b) have been studied by UV, CD, fluorescence, and proton NMR spectroscopy. Optical studies of a and b at dilute concentrations (microM range) yielded results similar to those seen for polymers of the same sequence, indicating th...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1991.10507857
更新日期:1991-04-01 00:00:00
abstract::The energetics of the B-Z transition of two different types of cloned alternating purine/pyrimidine DNA sequences have been analysed by a two dimensional electrophoretic technique. Since the transition between right handed and left handed forms of these polymers is detected by alterations of electrophoretic mobilities...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1983.10507467
更新日期:1983-12-01 00:00:00
abstract::Abstract In order to target the major groove of DNA, we have designed novel peptide derivatives of 7-H pyridocarbazole, which is the chromophoric ring of ditercalinium, a potent antitumor bisin- tercalator. We will present here the results obtained with a compound that has a D-Asn tethered to the pyridinium nitrogen...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1994.10508090
更新日期:1994-08-01 00:00:00
abstract::Tris-intercalation of an acridine trimer into the self-complementary dodecanucleotide d(CTTCGCGCGAAG) has been studied, in solution, by means of 1H and 31P nuclear magnetic resonance. In a first step all the non-exchangeable protons (except H5', H5"), the imino protons and seven of the eleven phosphorus have been assi...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1988.10506498
更新日期:1988-12-01 00:00:00
abstract::The amino acid sequences of the Yersinia pseudotuberculosis porin (YPS) and Y. pestis porin (YPT) have recently deduced but their three-dimensional structures were not known. These sequences were analyzed using the servers 3D-PSSM and PredPort. The YPS and YPT porins were shown to have a high degree of identity (above...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2005.10507056
更新日期:2005-10-01 00:00:00
abstract::Acid-induced structural changes of a mouse IgG2a monoclonal antibody (MN12) as indicated by Jiskoot et al. (Eur. J. Biochem. 201,223-232 (1991)) were studied by measuring the transient electric birefringence of MN12 in aqueous solution and in glycerol-water mixtures at different pH conditions. A multi-exponential anal...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1992.10507972
更新日期:1992-04-01 00:00:00
abstract::The molecular recognition and discrimination of very similar ligand moieties by proteins are important subjects in protein-ligand interaction studies. Specificity in the recognition of molecules is determined by the arrangement of protein and ligand atoms in space. The three pyrimidine bases, viz. cytosine, thymine, a...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2013.832384
更新日期:2014-01-01 00:00:00
abstract::Abstract Aromatic stacking of nucleic acid bases is one of the key players in determining the structure and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive overlap of their aromatic rings gave rise to numerous often contradictory suggestions about the physical origins of stacking and ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章,评审
doi:10.1080/07391102.2000.10506597
更新日期:2000-01-01 00:00:00
abstract::Alzheimer's disease (AD) is the most common progressive neurodegenerative brain disorder. It is characterized by the presence of extracellular aggregated fibrillary form of amyloid beta (Aβ) peptide and intraneuronal neurofibrillary tangles caused by the hyperphosphorylation of tau protein. Monomeric form of Aβ peptid...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1730970
更新日期:2020-03-02 00:00:00
abstract::Falcipain-2 (FP-2) is a member of papain family of cysteine proteases and the major hemoglobinase of the hemoglobin detoxification and hemozoin polymerization complex localized in the food vacuole of the plasmodium species. FP-2 is currently gaining clinical significance as the drug target of choice in combating malar...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2014.924878
更新日期:2015-01-01 00:00:00
abstract::Abstract The forces that direct protein folding lead naturally to native proteins and protein domains that are typically, to a first approximation, globular-spherical and compact, with a relatively clear distinction between the hydrophobic inside and polar outside. The near-universality of these features of protein ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2000.10506607
更新日期:2000-01-01 00:00:00
abstract::Notch is a single-pass transmembrane receptor protein. Delta (member of the DSL protein family), a Notch ligand, is also single-pass transmembrane protein that can interact with Notch to form the Delta-Notch complex. It has been demonstrated that of the 36 Epidermal Growth Factor (EGF) repeats of Notch, 11th and 12th ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2012.674184
更新日期:2012-01-01 00:00:00
abstract::Binding affinities of flavonols namely quercetin, myricetin, and kaempferol to human serum albumin (HSA) were determined fluorimetrically and the order was observed to be myricetin > quercetin > kaempferol demonstrating structure-activity relationship. Quercetin-coated silver nanoparticles (AgNPs) show higher binding ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1462732
更新日期:2019-04-01 00:00:00
abstract::The 1H NMR relaxation effects produced by paramagnetic Cr(III) complexes on nucleoside 5'-mono- and -triphosphates in D2O solution at pH' = 3 were measured. The paramagnetic probes were [Cr(III)(H2O)6]3+, [Cr(III)(H2O)3(HATP)], [Cr(III)(H2O)3(HCTP)] and [Cr(III)(H2O)3(UTP)-, while the matrix nucleotides (0.1 M) were H...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1990.10508529
更新日期:1990-02-01 00:00:00
abstract::Cell-division protein kinases (CDKs) are gorgeous examples of targets for the helpful treatment of cancer by using multi-target inhibitors. Specifically, targeting cell-division protein kinase1/cyclin B (CDK1/Cyclin B), cell-division protein kinase 2/cyclin A (CDK2/Cyclin A) and cell-division protein kinase 4/cyclin D...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1742792
更新日期:2020-03-24 00:00:00
abstract::X-chromosome-linked inhibitor of apoptosis (XIAP) inhibits cell apoptosis. Overexpression of XIAP is widely found in human cancers. Second mitochondria-derived activator of caspase (SMAC) protein inhibits XIAP through binding with Baculovirus Inhibitor of apoptosis protein Repeat (BIR) 3 or BIR2 domain of XIAP. In thi...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1713892
更新日期:2021-02-01 00:00:00
abstract::Eukaryotic translation initiation factors (eIFs) are the group of regulatory proteins that are involved in the initiation of translation events. Among them, eIF4A1, a member of the DEAD-box RNA helicase family, participates in a wide spectrum of activities which include, RNA splicing, ribosome biogenesis, and RNA degr...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1751295
更新日期:2020-05-05 00:00:00
abstract::In order to examine whether chiral metal complexes can be used to discriminate between right- and left-handed DNA conformational states we have studied the enantioselective interactions of Fe(phen)3(2+) and Ru(phen)3(2+) (phen = 1,10-phenanthroline) with poly(dGm5dC) under B- and Z-form conditions. With the inversion-...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1987.10506377
更新日期:1987-08-01 00:00:00
abstract::Abstract Although the recent structural studies on polymerases have brought new insights on polymerase fidelity, the role of DNA sequence and structure is not well understood. Here, the analysis of the crystal structures of hotspots for polymerase slippage shows that, in the B- form, these sequences share common str...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2000.10506617
更新日期:2000-01-01 00:00:00
abstract::Inspection of stereochemical models suggests a possible correlation between the proportion (Yg-/Yt) of the g- and t rotamers and the S pucker populations irrespective of the anti-syn conformational composition of the base. Interpretation of the NMR vicinal coupling constants in terms of conformational populations show...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1984.10507558
更新日期:1984-08-01 00:00:00