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*  An improved sequence-based prediction protocol for protein-protein interactions using amino acids substitution matrix and...
In this article, a sequence-based approach is proposed by combining a novel amino acid substitution matrix feature ... An improved sequence-based prediction protocol for protein-protein interactions using amino acids substitution matrix and ...
http://ira.lib.polyu.edu.hk/handle/10397/65689
*  Maximum Parsimony (Construct Phylogeny)
By default, all nucleotide (or amino acid) changes are weighted equally in MEGA (standard parsimony). However, for nucleotide ... For a given topology, the sum of the minimum possible substitutions over all sites is known as the Tree Length. The topology ...
http://www.megasoftware.net/mega4/WebHelp/hc_maximum_parsimony.htm
*  Two types of amino acid substitutions in protein evolution | SpringerLink
... decreases linearly with the increase in physico-chemical differences between amino acid pairs involved in a... ... The frequency of amino acid substitutions, relative to the frequency expected by chance, ... Amino acid substitution Physico-chemical difference Conservative Low-constraint Protein evolution This is a preview of ... The frequency of amino acid substitutions, relative to the frequency expected by chance, decreases linearly with the increase ...
https://link.springer.com/article/10.1007%2FBF01732340
*  PLOS ONE: Predicting the Functional Effect of Amino Acid Substitutions and Indels
... tools primarily focus on studying the deleterious effects of single amino acid substitutions through examining amino acid ... and multiple amino acid substitutions. This alignment-based score measures the change in sequence similarity of a query ... score as a new metric to predict the damaging effects of variations not limited to single amino acid substitutions but also in- ... approach to predict the functional effects of protein sequence variations including single or multiple amino acid substitutions ...
https://journals.plos.org/plosone/article/figure?id=10.1371/journal.pone.0046688.g010
*  Feature-Based Classification of Amino Acid Substitutions outside Conserved Functional Protein Domains
PolyPhen-2 and SIFT had significantly lower accuracies in predicting the effects of amino acid substitutions outside CFDs than ... There are more than 500 amino acid substitutions in each human genome, and bioinformatics tools irreplaceably contribute to ... Feature-Based Classification of Amino Acid Substitutions outside Conserved Functional Protein Domains. Branislava Gemovic, ... are more suitable for the classification of amino acid substitutions outside CFDs than phylogeny-based tools. ...
https://www.hindawi.com/journals/tswj/2013/948617/abs/
*  Figure 3: Giraffe genes and pathways exhibiting extraordinary divergence and patterns of amino acid substitutions.
a) Giraffe FGFRL1 contains seven amino acid substitutions that are unique at fixed sites in other mammals and/or are predicted ... Figure 3 : Giraffe genes and pathways exhibiting extraordinary divergence and patterns of amino acid substitutions.. From: ... The giraffe and okapi MDC1 gene exhibits a 264 amino acid deletion that removes part of the SDT region that harbours two ... The unique substitution in giraffe, G234Q, immediately adjacent to the Gpi anchor site may alter the anchor site or the rate of ...
https://www.nature.com/articles/ncomms11519/figures/3?error=cookies_not_supported&code=4bfc5263-f281-4a0c-bf67-903aacd76662
*  Comment on "Transitions to Asexuality Result in Excess Amino Acid Substitutions" | Science
Paland and Lynch (1) demonstrated this effect in Daphnia pulex by showing that the rates of amino acid replacement substitution ... Comment on 'Transitions to Asexuality Result in Excess Amino Acid Substitutions' Message Subject. (Your Name) has forwarded a ... A class of moderately deleterious amino acid substitutions has a higher probability of spreading to fixation in asexual ... the ratio of amino acid replacement to silent substitution in mitochondrial genes is higher in asexual lineages than in sexual ...
http://science.sciencemag.org/content/313/5792/1389.2
*  Evaluating the efficacy of a structure-derived amino acid substitution | AABC
Here we present amino acid substitution matrices constructed from the alignment of a large number of protein domain structures ... Homology search algorithms employ amino acid substitution matrices to detect similarity between proteins sequences. The ... Keywords: computational biology, protein homology, amino acid substitution matrix, protein structure ... We show that when incorporated into the homology search algorithms BLAST and PSI-blaST, the structure-based substitution ...
https://www.dovepress.com/evaluating-the-efficacy-of-a-structure-derived-amino-acid-substitution-a3236
*  Predicting the functional effect of amino acid substitutions and indels. | J. Craig Venter Institute
... tools primarily focus on studying the deleterious effects of single amino acid substitutions through examining amino acid ... and multiple amino acid substitutions. This alignment-based score measures the change in sequence similarity of a query ... score as a new metric to predict the damaging effects of variations not limited to single amino acid substitutions but also in- ... approach to predict the functional effects of protein sequence variations including single or multiple amino acid substitutions ...
https://www.jcvi.org/publications/predicting-functional-effect-amino-acid-substitutions-and-indels
*  Amino-Acid Substitutions In Membrane Proteins: Applications To Homology Recognition And Comparative Modelling | Sciweavers
Amino-Acid Substitutions In Membrane Proteins: Applications To Homology Recognition And Comparative Modelling - ent, ,title,,p, ... Amino-Acid Substitutions In Membrane Proteins: Applications To Homology Recognition And Comparative Modelling. ... A novel series of compositionally biased substitution matrices for comparing Plasmodium pr... ...
http://www.sciweavers.org/publications/amino-acid-substitutions-membrane-proteins-applications-homology-recognition-and-compar
*  Frontiers | PASE: a novel method for functional prediction of amino acid substitutions based on physicochemical properties |...
Evaluation of PASE, using a few amino acid substitutions of known phenotypic effects and 3338 human amino acid substitutions, ... Evaluation of PASE, using a few amino acid substitutions of known phenotypic effects and 3338 human amino acid substitutions, ... Results: Here we present PASE, a novel method that predicts the effect of an amino acid substitutions based on physicochemical ... Thus, there is a strong need for efficient bioinformatics tools to predict the functional effect of amino acid substitutions. ...
https://www.frontiersin.org/articles/10.3389/fgene.2013.00021/full
*  The effects of amino acid substitution on apomyoglobin stability, folding intermediates, and holoprotein expression
... ... and helix propensity of the replacement amino acid. In most cases, once a range of amino acids has been correlated at a given ... "The effects of amino acid substitution on apomyoglobin stability, folding intermediates, and holoprotein expression." (2003) ... unfolding constants of the corresponding single mutants or from the amino acid properties of the substituted amino acid using ...
https://scholarship.rice.edu/handle/1911/18562
*  Distribution of non-synonymous amino acid substitutions | Open-i
Distribution of non-synonymous amino acid substitutions across Odorant Receptor (OR) domains. a The white bars represent the ... Fig3: Distribution of non-synonymous amino acid substitutions across Odorant Receptor (OR) domains. a The white bars represent ... Fig3: Distribution of non-synonymous amino acid substitutions across Odorant Receptor (OR) domains. a The white bars represent ... 3) which covered between 19.3 % and 35.8 % of the OR amino acid sequence (Mean: 30.5 %; Additional file 1: Table S6). ...
https://openi.nlm.nih.gov/detailedresult.php?img=PMC4552289_12862_2015_451_Fig3_HTML&req=4
*  Data from: Sequence entropy of folding and the absolute rate of amino acid substitutions - Dryad
Data from: Sequence entropy of folding and the absolute rate of amino acid substitutions. Dryad Repository. ... Goldstein RA, Pollock DD (2017) Data from: Sequence entropy of folding and the absolute rate of amino acid substitutions. Dryad ... Here we use parallels between amino acid substitutions and chemical reaction kinetics to develop an improved theory of protein ... Goldstein RA, Pollock DD (2017) Sequence entropy of folding and the absolute rate of amino acid substitutions. Nature Ecology ...
http://datadryad.org/resource/doi:10.5061/dryad.7b8vb
*  Viruses | Free Full-Text | Single Amino Acid Substitution N659D in HIV-2 Envelope Glycoprotein (Env) Impairs Viral Release and...
We also tested a virus presenting a truncation of 109 amino acids at the C-terminal part of Env, a cytoplasmic tail partial ... Single Amino Acid Substitution N659D in HIV-2 Envelope Glycoprotein (Env) Impairs Viral Release and Hampers BST-2 Antagonism. ... "Single Amino Acid Substitution N659D in HIV-2 Envelope Glycoprotein (Env) Impairs Viral Release and Hampers BST-2 Antagonism." ... Dufrasne, F.E.; Lombard, C.; Goubau, P.; Ruelle, J. Single Amino Acid Substitution N659D in HIV-2 Envelope Glycoprotein (Env) ...
http://www.mdpi.com/1999-4915/8/10/285
*  RCSB PDB - 1LYF: DISSECTION OF HELIX CAPPING IN T4 LYSOZYME BY STRUCTURAL AND THERMODYNAMIC ANALYSIS OF SIX AMINO...
Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of six amino acid substitutions at Thr 59. ... DISSECTION OF HELIX CAPPING IN T4 LYSOZYME BY STRUCTURAL AND THERMODYNAMIC ANALYSIS OF SIX AMINO ACID SUBSTITUTIONS AT THR 59. ...
http://www.rcsb.org/pdb/explore/litView.do?structureId=1LYF
*  Structure Cluster - 1LYG: DISSECTION OF HELIX CAPPING IN T4 LYSOZYME BY STRUCTURAL AND THERMODYNAMIC ANALYSIS OF SIX...
Dissection of helix capping in T4 lysozyme by structural and thermodynamic analysis of six amino acid substitutions at Thr 59. ... DISSECTION OF HELIX CAPPING IN T4 LYSOZYME BY STRUCTURAL AND THERMODYNAMIC ANALYSIS OF SIX AMINO ACID SUBSTITUTIONS AT THR 59. ... Acids Res. 2008 36: D419-D425 * [4] Alexandrov N., Shindyalov I. (2003). PDP: protein domain parser.. Bioinformatics 2003 Feb; ...
http://www.rcsb.org/pdb/explore/structureCluster.do?structureId=1LYG
*  IJMS | Free Full-Text | The Triple Amino Acid Substitution TAP-IVS in the EPSPS Gene Confers High Glyphosate Resistance to the...
In addition, a novel triple amino acid substitution from TAP (wild type, GSH) to IVS (triple mutant, GRH) was identified in the ... The nucleotide substitutions consisted of ATA102, GTC103 and TCA106 instead of ACA102, GCG103, and CCA106, respectively. The ... "The Triple Amino Acid Substitution TAP-IVS in the EPSPS Gene Confers High Glyphosate Resistance to the Superweed Amaranthus ... The Triple Amino Acid Substitution TAP-IVS in the EPSPS Gene Confers High Glyphosate Resistance to the Superweed Amaranthus ...
https://www.mdpi.com/1422-0067/20/10/2396
*  Evidence that the Origin of Naked Kernels During Maize Domestication Was Caused by a Single Amino Acid Substitution in tga1 |...
Evidence that the Origin of Naked Kernels During Maize Domestication Was Caused by a Single Amino Acid Substitution in tga1. ... Evidence that the Origin of Naked Kernels During Maize Domestication Was Caused by a Single Amino Acid Substitution in tga1. ... Evidence that the Origin of Naked Kernels During Maize Domestication Was Caused by a Single Amino Acid Substitution in tga1. ... Evidence that the Origin of Naked Kernels During Maize Domestication Was Caused by a Single Amino Acid Substitution in tga1 ...
http://www.genetics.org/content/early/2015/05/04/genetics.115.175752
*  Abrogation of CTL Epitope Processing by Single Amino Acid Substitution Flanking the C-Terminal Proteasome Cleavage Site | The...
Abrogation of CTL Epitope Processing by Single Amino Acid Substitution Flanking the C-Terminal Proteasome Cleavage Site. Nico J ... Abrogation of CTL Epitope Processing by Single Amino Acid Substitution Flanking the C-Terminal Proteasome Cleavage Site ... Abrogation of CTL Epitope Processing by Single Amino Acid Substitution Flanking the C-Terminal Proteasome Cleavage Site ... Abrogation of CTL Epitope Processing by Single Amino Acid Substitution Flanking the C-Terminal Proteasome Cleavage Site ...
http://www.jimmunol.org/content/164/4/1898.long
*  Frontiers | The Amino Acid Substitution Q65H in the 2C Protein of Swine Vesicular Disease Virus Confers Resistance to Golgi...
A single amino acid substitution, Q65H, in the non-structural protein 2C was found to be responsible for increased resistance ... A single amino acid substitution, Q65H, in the non-structural protein 2C was found to be responsible for increased resistance ... Figure 7. The amino acid substitution Q65H in 2C confers resistance to GCA. IBRS-2 cells treated with 10 μM GCA for 30 min were ... The Amino Acid Substitution Q65H in the SVDV 2C Protein Also Confers Resistance to GCA. The production of SVDV was inhibited by ...
https://www.frontiersin.org/articles/10.3389/fmicb.2016.00612/full
*  Eurosurveillance | Y155H amino acid substitution in influenza A(H1N1)pdm09 viruses does not confer a phenotype of reduced...
We believe that this report can contribute to a better understanding of the biological significance of amino acid substitutions ... During the 2012/13 epidemic season in Spain, two A(H1N1)pdm09 viruses bearing the specific Y155H substitution in the NA were ... The Y155H amino acid substitution in the neuraminidase gene (NA) has previously been associated with highly reduced inhibition ... Y155H amino acid substitution in influenza A(H1N1)pdm09 viruses does not confer a phenotype of reduced susceptibility to ...
http://www.eurosurveillance.org/content/10.2807/1560-7917.ES2014.19.27.20849
*  Specific Amino Acid Substitutions in the Proline-Rich Motif of the Rhizobium meliloti ExoP Protein Result in Enhanced...
Two of seven amino acid substitutions in the proline-rich motif of ExoP affected EPS I production, indicating that most of the ... Substitution of specific amino acid residues in the proline-rich motif of the ExoP protein.To analyze the relevance of the ... Specific Amino Acid Substitutions in the Proline-Rich Motif of the Rhizobium meliloti ExoP Protein Result in Enhanced ... D) Single substitutions of amino acid residues of the ExoP protein. Numbers below the partial ExoP sequence indicate the ...
https://jb.asm.org/content/180/2/395?ijkey=09b3e80ca266bd3ad3966c69817ad1f123c278a4&keytype2=tf_ipsecsha
*  A single amino acid substitution in the alpha 3 domain of an H-2 class I molecule abrogates reactivity with CTL. | JEM
A single amino acid substitution in the alpha 3 domain of an H-2 class I molecule abrogates reactivity with CTL.. T A Potter, J ... A single amino acid substitution in the alpha 3 domain of an H-2 class I molecule abrogates reactivity with CTL. ... of this somatic cell variant was sequenced and a single nucleotide change resulting in a glutamic acid to lysine substitution ...
http://jem.rupress.org/content/166/4/956