predicted secondary structure elements
RNA Structures Facilitate Recombination-Mediated Gene Swapping in HIV-1
... RNA secondary structure elements might influence natural recombination patterns, we reanalyzed the locations of recom- bination breakpoints within an alignment of near-full-length genome sequences ...
8
An algorithm to parse segment packing in predicted protein contact maps
... two secondary structure elements in a contact map, The diagonal/ orthogonal trend can be quantified by the strength of fit of a regression line in each ...
12
Proposing a highly accurate protein structural class predictor using segmentation - based features
... use predicted secondary structure using SPINE-X which was recently proposed by [44] and attained better results than PSIPRED on predicting pro- tein secondary structure (especially for ...
13
Structural Analysis of Predicted HIV 1 Secis Elements
... SECIS elements obtained, we designed their secondary structures based on the RNA secondary structure (folding) prediction algorithm given by ...possible secondary structures based on ...
11
Secondary Structural Elements within the 3′ Untranslated Region of Mouse Hepatitis Virus Strain JHM Genomic RNA
... RNA secondary structure within the 3⬘-terminal 166 nt of the MHV-JHM genome in ...structural elements identified by enzymatic probing exist in the context of a larger RNA molecule and to explore ...
9
The Relationship Between Third-Codon Position Nucleotide Content, Codon Bias, mRNA Secondary Structure and Gene Expression in the Drosophilid Alcohol Dehydrogenase Genes Adh and Adhr
... mRNA secondary structure, third-codon position nucleotide distribution, and gene expression, we predicted secondary structures in two related drosophilid genes, Adh and Adhr, which differ in ...
12
Mutagenic Analysis of the 3′ cis-Acting Elements of the Rubella Virus Genome
... Thermodynamically predicted secondary structure analysis of the 3 * -terminal 305 nucleotides (nt) of the rubella virus (RUB) genome, a region conserved in all RUB defective interfering RNAs, ...
18
Examining the Process of de Novo Gene Birth: An Educational Primer on “Integration of New Genes into Cellular Networks, and Their Structural Maturation”
... or structure of a ...protein structure) of a predicted protein is determined by the genetic code or the codons within the boundaries of the open reading frame of the ...protein structure is a ...
7
Environmental factors modulating the stability and enzymatic activity of the Petrotoga mobilis Esterase (PmEst)
... strands elements (Fig 3), due to the presence of the two minima at the region of 222 and 208 nm, and the positive maximum at 196 nm that are charac- teristic spectral bands for α -helices [38 – 39], and the ...
17
Prediction of similar transforming regions in simian virus 40 large T, adenovirus E1A, and myc oncoproteins.
... 1814 Downloaded from http://jvi.asm.org/ on November 10, 2019 by guest Regions containing similar elements of primary and predicted secondary structure were identified in simian virus 40[r] ...
5
Conservation and Divergence of the I-Domain Inserted into the Ubiquitous HK97 Coat Protein Fold in P22-Like Bacteriophages
... in structure elements at the periphery of the conserved fold, (ii) in the locations of dis- ordered loops important in capsid assembly and conformational transitions, (iii) in surfaces charges, and (iv) in ...
14
ATPsite: sequence-based prediction of ATP-binding residues
... The architecture of the ATPsite predictor is shown in Figure 1. For a given protein sequence, PSIPRED [11] is used to predict the secondary structure, REAL Spine3 [12] predicts the RSA values and dihedral ...
8
Predicting Βeta Turns and Βeta Turn Types Using a Novel Over Sampling Approach
... β -turn is one of the most common tight turns. It is composed of four consecutive residues that are not in an α -helix and the distance between the first and the fourth C_ α is less than 7 Å [1]. β -turns play an ...
15
Functional analysis of human T-cell leukemia virus type I rex-response element: direct RNA binding of Rex protein correlates with in vivo activity.
... The correlation between our in vivo results and the direct binding of Rex protein to mutant and wild-type RxRE sequences supports both the existence of the predicted secondary structure [r] ...
6
Hyperthermophilic Protein Scaffolds for Engineering Biomolecular Recognition.
... recognition, adding to the palate of alternate scaffolds available for generating binding proteins. Mutant proteins derived from scaffolds in the super-library have several desirable properties such as low molecular ...
269
The 5' nontranslated region of hepatitis A virus RNA: secondary structure and elements required for translation in vitro.
... Nucleotide substitutions in specific virus strains from the wild-type HM175 sequence are shown in boldface type; base pairs identified by covariant substitutions among all nine strains a[r] ...
11
Toward a Database of Geometric Interrelationships of Protein Secondary Structure Elements for De Novo Protein Design, Prediction and Analysis
... ProtCAD stands for Protein Computer Assisted Design. It is a software library of object-oriented general-purpose protein modeling and analysis tools written in C++ by my thesis advisor Christopher Summa. It was ...
61
Description and initial characterization of metatranscriptomic nidovirus-like genomes from the proposed new family Abyssoviridae, and from a sister group to the Coronavirinae, the proposed genus Alphaletovirus
... predicted transmembrane regions, and predicted protein secondary structure is 555. shown in Fig[r] ...
40
<p>In silico Analysis, Molecular Docking, Molecular Dynamic, Cloning, Expression and Purification of Chimeric Protein in Colorectal Cancer Treatment</p>
... protein was done using advanced modeling based on mul- tiple templates with Modeller9.20. 21 Since the chimeric protein possesses domains from two proteins (CD326 and CD166), the templates 4MZV A and 5A2F A were utilized ...
21
Physical and functional analysis of genes from the CAM catabolic plasmid encoding probable steps in the catabolism of camphor
... Two different approaches were used to determine potential open reading frames and coding regions on the 4485-bp DNA sequence. The first approach is the FramePlot2.3.2 program developed by Ishikawa and Hotta (1999). ...
288