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*  Ancestral reconstruction
On a molecular level, amino acid residues at different locations of a protein may evolve non-independently because they have a ... One may also use this substitution model as the basis for a Bayesian inference procedure, which would consider the posterior ... Pupko, T.; Pe, I.; Shamir, R.; Graur, D. (2000). "A Fast Algorithm for Joint Reconstruction of Ancestral Amino Acid Sequences ... Motivated by the development of techniques for determining the primary (amino acid) sequence of proteins by Frederick Sanger in ...
*  Molecular phylogenetics
A comprehensive step-by-step protocol on constructing phylogenetic tree, including DNA/Amino Acid contiguous sequence assembly ... by dividing the number of substitutions by the number of base pairs analysed: the hope is that this measure will be independent ... for example the insertion of a section of nucleic acid in one haplotype that is not present in another). The difference between ... This is referred to as the number of substitutions (other kinds of differences between haplotypes can also occur, ...
*  Nucleic acid sequence
The absence of substitutions, or the presence of only very conservative substitutions (that is, the substitution of amino acids ... ISBN 0-87969-608-7. Ng, P. C.; Henikoff, S. (2001). "Predicting Deleterious Amino Acid Substitutions". Genome Research. 11 (5 ... The sequence of nucleobases on a nucleic acid strand is translated by cell machinery into a sequence of amino acids making up a ... Each group of three bases, called a codon, corresponds to a single amino acid, and there is a specific genetic code by which ...
*  Sequence alignment
The absence of substitutions, or the presence of only very conservative substitutions (that is, the substitution of amino acids ... color is often used to indicate amino acid properties to aid in judging the conservation of a given amino acid substitution. ... In typical usage, protein alignments use a substitution matrix to assign scores to amino-acid matches or mismatches, and a gap ... Ng PC; Henikoff S (May 2001). "Predicting deleterious amino acid substitutions". Genome Res. 11 (5): 863-74. doi:10.1101/gr. ...
*  CORIN
The amino acid substitutions impaired corin activity. An insertion variant in exon 1 alters the cytoplasmic tail. This variant ... Human corin, a polypeptide of 1042 amino acids, consists of an N-terminal cytoplasmic domain, a transmembrane domain and an ...
*  Substitution matrix
Many specialized substitution matrices have been developed that describe the amino acid substitution rates in specific ... Each amino acid is more or less likely to mutate into various other amino acids. For instance, a hydrophilic residue such as ... and you will often see the same substitution matrix expressed in different bases. One of the first amino acid substitution ... th amino acid being transformed into the j {\displaystyle j} th amino acid in a certain amount of evolutionary time. There are ...
*  BLOSUM
Two major forces drive the amino-acid substitution rates away from uniformity: substitutions occur with the different ... However, these amino acids can be categorised into groups with similar physicochemical properties. Substituting an amino acid ... Substitution matrices for amino acids are more complicated and implicitly take into account everything that might affect the ... Then, they calculated a log-odds score for each of the 210 possible substitution pairs of the 20 standard amino acids. All ...
*  Steven Henikoff
"Amino Acid Substitution Matrices from Protein Blocks". PNAS. 89 (22): 10915-10919. doi:10.1073/pnas.89.22.10915. PMC 50453 . ... In 1992, Steven Henikoff, together with his wife Jorja Henikoff, introduced the BLOSUM substitution matrices. The BLOSUM ...
*  Phage P22 Tailspike Protein
Mitraki A, King J (Jul 1992). "Amino acid substitutions influencing intracellular protein folding pathways". FEBS Letters. 307 ... P22TSP is a homotrimeric structural protein consisting of 666 amino acids. It is noncovalently bound to the neck of the viral ... Two aspartic acids and one glutamic acid in the active site have been strongly linked to enzymatic activity. Different ...
*  CS-BLAST
Similarities between amino acids or nucleotides are quantified in these substitution matrices. The substitution score ( S {\ ... mutating into amino acid b {\displaystyle b} [2]. In a large set of sequence alignments, counting the number of amino acids as ... "Discriminative Modelling of Context-specific Amino Acid Substitution Properties" BIOINFORMATICS 28.24 (2012): 3240-247. Oxford ... In predicting substitution probabilities using only the amino acid's local sequence context, you gain the advantage of not ...
*  List of sequence alignment software
"Discriminative modelling of context-specific amino acid substitution probabilities". Bioinformatics. 28 (24): 3240-7. doi: ... September 1997). "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs". Nucleic Acids Research. 25 ... 1998). Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge, UK: Cambridge University ... Nucleic Acids Research. 34 (17): e112. doi:10.1093/nar/gkl480. PMC 1635247 . PMID 16971460. Girdea, M; Noe, L; Kucherov, G ( ...
*  Julian Gough (scientist)
"Predicting the functional consequences of cancer-associated amino acid substitutions". Bioinformatics. 29 (12): 1504-10. doi: ... His research has been published in leading peer reviewed scientific journals including Nature, Science, Cell, Nucleic Acids ... 2005). "InterPro, progress and status in 2005". Nucleic Acids Research. 33 (Database issue): D201-5. doi:10.1093/nar/gki106. ... SCOP sequence searches, alignments and genome assignments". Nucleic Acids Research. 30 (1): 268-272. doi:10.1093/nar/30.1.268. ...
*  Pyruvate dehydrogenase (lipoamide) alpha 1
Takakubo F, Cartwright P, Hoogenraad N, Thorburn DR, Collins F, Lithgow T, Dahl HH (Oct 1995). "An amino acid substitution in ... Structural implications of novel amino acid substitutions in E1 protein". Molecular Genetics and Metabolism. 104 (4): 507-16. ... The preliminary peptide encoded by this gene was 29 amino acids at the very start of the sequence that correspond to a typical ... The remaining 361 amino acids, starting at the N terminus with phenylalanine, represent the mature mitochondrial E1 alpha ...
*  Mastoparan
"Selective amino acid substitution reduces cytotoxicity of the antimicrobial peptide mastoparan". Biochimica et Biophysica Acta ...
*  Smith-Waterman algorithm
Different base substitutions or amino acid substitutions can have different scores. The substitution matrix of amino acids is ... Each base substitution or amino acid substitution is assigned a score. In general, matches are assigned positive scores, and ... A substitution matrix assigns each pair of bases or amino acids a score for match or mismatch. Usually matches get positive ... Saul B. Needleman; Christian D. Wunsch (1970). "A general method applicable to the search for similarities in the amino acid ...
*  Substitution model
Since not all DNA substitution also alter the encoded amino acid, information is lost when looking at amino acids instead of ... for an amino acid sequence (there are 20 "standard" amino acids that make up proteins), you would find there are 208 parameters ... "Higher rates of amino acid substitution in rodents than in humans". Mol. Phylogenet. Evol. 1 (3): 211-4. doi:10.1016/1055-7903( ... Unlike the DNA models, amino acid models traditionally are empirical models. They were pioneered in the 1970s by Dayhoff and co ...
*  Models of DNA evolution
Gu X, Li W (1992). "Higher rates of amino acid substitution in rodents than in man". Molecular Phylogenetics and Evolution. 1 ( ... for an amino acid sequence (there are 20 "standard" amino acids that make up proteins), one would find there are 209 parameters ... a codon is three bases and codes for one amino acid in a protein). There are 4 3 = 64 {\displaystyle 4^{3}=64} codons, but the ... These substitution models differ in terms of the parameters used to describe the rates at which one nucleotide replaces another ...
*  Phosphoenolpyruvate carboxylase
"Greater efficiency of photosynthetic carbon fixation due to single amino-acid substitution". Nature Communications. 4 (2): 1518 ... The sequence length is about 966 amino acids. See figure 1 for a PyMOL generated structure of the enzyme's single subunit from ... It includes a conserved aspartic acid (D564) and a glutamic acid (E566) residue that non-covalently bind a divalent metal ... such as for example amino acids. PEP carboxylase is mainly subject to two levels of regulation: phosphorylation and allostery. ...
*  Beta-lactamase
... such as clavulanic acid. Single amino acid substitutions at positions 104, 164, 238, and 240 produce the ESBL phenotype, but ... Amino acid substitutions in OXA enzymes can also give the ESBL phenotype. While most ESBLs have been found in E. coli, K. ... Ten variants, KPC-2 through KPC-11 are known, and they are distinguished by one or two amino acid substitutions (KPC-1 was re- ... The amino acid substitutions responsible for the extended-spectrum beta lactamase (ESBL) phenotype cluster around the active ...
*  Character evolution
Character state changes can be phenotypic changes, nucleotide substitutions, or amino acid substitutions. These small changes ...
*  Cysteine
Betts, M.J.; R.B. Russell (2003). "Hydrophobic amino acids". Amino Acid Properties and Consequences of Substitutions, In: ... Non-Polar Amino Acids". Archived from the original on 2012-09-05. Retrieved 2012-09-16. "Virtual Chembook--Amino Acid Structure ... so it must be biosynthesized from its constituent amino acids, cysteine, glycine and glutamic acid. Glutamic acid and glycine ... interactions in micelles to a greater degree than the side chain in the non-polar amino acid glycine and the polar amino acid ...
*  Susan Rae Wente
8 August 1986). "Effect of amino acid substitutions on the catalytic and regulatory properties of aspartate transcarbamoylase ... Wente and her colleagues investigated the enzyme aspartate transcarbamoylase and the amino acid residues that assist in making ...
*  R.EcoRII
A single amino acid substitution uncouples target recognition from cooperative DNA interaction and cleavage". J. Biol. Chem. ... Its molecular mass is 45.2 kDa, being composed of 402 amino acids. EcoRII is a bacterial Type IIE REase that interacts with two ... 2003). "A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes". Nucleic Acids ... Nucleic Acids Research. 35 (7): 2227-37. doi:10.1093/nar/gkm045. PMC 1874628 . PMID 17369272. Molecular and Cellular Biology ...
*  SNP annotation
... predicting effects of amino acid substitutions on proteins". Nucleic Acids Res. 2012: W452-W457. doi:10.1093/nar/gks539. ... Ng P. C.; Henikoff S. (2003). "SIFT: predicting amino acid changes that affect protein function". Nucleic Acids Research. 31 ( ... Non-synonymous is the variant in exons that change the amino acid sequence encoded by the gene, including single base changes ... Yates, C. M.; Filippis, I.; Kelley, L. A.; Sternberg, M. J. (2014). "SuSPect: enhanced prediction of single amino acid variant ...
*  Myeong-Hee Yu
Kwon, K.S.; Kim, J; shin, H.S.; Yu, M.H. (1 April 1994). "Single amino acid substitutions of alpha 1-antitrypsin that confer ... Yu and her research team have worked to discover what amino acids can suppress certain types of mutations, such as the tsf ...
*  Shiladitya DasSarma
DasSarma, Shiladitya; Capes, Melinda D.; Karan, Ram; DasSarma, Priya (2013-03-11). "Amino Acid Substitutions in Cold-Adapted ...
*  PANTHER
... this substitutions should be entered in the standard amino acid substitution format, e.g. L46P. PANTHER will use an alignment ... You must enter a protein sequence in the first box and the substitutions relative to this protein sequence in the second box; ... Jan 2012). "InterPro in 2011: new developments in the family and domain prediction database". Nucleic Acids Res. 40 (Database ... Aug 2013). "Large-scale gene function analysis with the PANTHER classification system". Nucleic Acids Res. 8 (8): 1551-66. doi: ...