Loading...
*  Profile of Steven Henikoff | PNAS
They called their technique BLOSUM, for BLOcks of Amino Acid SUbstitution Matrix. ... Recently, Henikoff's group has introduced methods to help researchers take advantage of burgeoning DNA sequence resources. One ... 1992) Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 89:10915-10919.. ... Henikoff found Meselson to be an incredibly creative thinker who got Henikoff started on what would become his life's work. One ...
  https://www.pnas.org/content/104/50/19665
*  BLOSUM - Wikipedia
Sequence alignment Point accepted mutation Henikoff, S.; Henikoff, J.G. (1992). "Amino Acid Substitution Matrices from Protein ... Henikoff and Henikoff introduced BLOSUM (BLOcks SUbstitution Matrix) matrix which led to marked improvements in alignments and ... BLOSUM matrices were first introduced in a paper by Steven Henikoff and Jorja Henikoff. They scanned the BLOCKS database for ... However, these amino acids can be categorised into groups with similar physicochemical properties. Substituting an amino acid ...
  https://en.wikipedia.org/wiki/BLOSUM
*  Steven Henikoff - Wikipedia
In 1992, Steven Henikoff, together with his wife Jorja Henikoff, introduced the BLOSUM substitution matrices. The BLOSUM ... sharedresources.fredhutch.org/profile/henikoff-steven Henikoff, S.; Henikoff, J.G. (1992). "Amino Acid Substitution Matrices ... Steven Henikoff is a scientist at the Fred Hutchinson Cancer Research Center, and an HHMI Investigator. His field of study is ... In 2005, Henikoff was elected to the National Academy of Sciences. http://research.fhcrc.org/henikoff/en.html http://www.hhmi. ...
  https://en.wikipedia.org/wiki/Steven_Henikoff
*  User:Jarle Pahr/Bioinformatics - OpenWetWare
http://en.wikipedia.org/wiki/BLOSUM Article: S Henikoff and J G Henikoff, 1992. Amino acid substitution matrices from protein ... which is associated with introducing a gap in the alignment. ... Substitution frequencies for all possible pairs of amino acids ... Block Substitution Matrices (BLOSUM): Developed in the 1990s using local multiple alignments. A set of aligned highly conserved ... Structure predictions are made by "threading" (aligning) each amino acid in the target sequence to one of several templates and ...
  https://openwetware.org/wiki/User:Jarle_Pahr/Bioinformatics
*  关于同源、相似性、相似性矩阵和点阵图 - 序列
Let's take amino acids as an exmple. They can be divided into several groups based on their chemical properties, such as ... and worked out several BLOSUM matrices. The most commonly used scoring matrix for protein alignment nowadays may be the BLOSUM ... We self-multiply the transition probability matrix, which will be briefly introduced here and may be introduced in detail in ... Steven Henikoff and Dr. Jorja Henikoof did similar work based on much more multiple sequence alignments. ...
  https://www.coursera.org/learn/sheng-wu-xin-xi-xue/lecture/SXgsC/guan-yu-tong-yuan-xiang-si-xing-xiang-si-xing-ju-zhen-he-dian-zhen-tu
*  Indian Patents. 235712:'A PURIFIED MODIFIED IL-4 MUREIN RECEPTOR ANTAGONIST'
... wherein the amino acid residue designated as X may be any amino acid residue except proline. The substitution of amino acid ... Henikoff et al, 1992, Proc. Natl Acad. Sci USA, 89:10915-10919 for the BLOSUM 62 comparison matrix) is also used by the ... Such techniques can be used to introduce one or more exogenous DNA moieties into suitable host cells.. The term "transformation ... D-amino acids) of the twenty conventional amino acids; unnatural amino acids such as a-, a-disubstituted amino acids, N-alkyl ...
  http://www.allindianpatents.com/patents/235712-a-purified-modified-il-4-murein-receptor-antagonist
*  Point accepted mutation - Wikipedia
Henikoff S, Henikoff JG (1992). "Amino acid substitution matrices from protein blocks" (PDF). Proceedings of the National ... mutation events to occur per 100 amino acids. PAM matrices were introduced by Margaret Dayhoff in 1978. The calculation of ... This is known as a BLOSUM. The two result in the same scoring outcome, but use differing methodologies. BLOSUM directly look at ... th amino acid with the i {\displaystyle i} th amino acid, to the probability of these amino acids being aligned by chance. The ...
  https://en.wikipedia.org/wiki/Point_accepted_mutation
*  Patent US7384738 - Retrovirus-based genomic screening - Google Patents
... is then introduced into a retroviral packaging cell. The resulting provirus or proteins expression from the provirus are then ... as well as proteins encoded by homologous genes having amino acid substitutions that cause decreased (e.g., null mutations) ... and Henikoff, J. G., Genomics, 19:97 [1994]; Henikoff, J. G. and Henikoff, S., Meth. Enz., 266:88 [1996]. ... The BLOSUM (Blocks Substitution Matrix) series of matrices are constructed based on percent identity between two sequence ...
  http://www.google.com/patents/US7384738?dq=5,966,702
*  Patent US7074590 - Chimeric promoters - Google Patents
For amino acid alignments, the BLOSUM algorithm can be used as a protein weight matrix (Henikoff and Henikoff, (1992) Proc Natl ... Alternatively, the nucleic acid or vector can be introduced into the cells of the subject by administering the nucleic acid or ... substitution, and/or deletion of one or more nucleotides and nucleic acids that are otherwise modified. Preferably, fragments, ... of a selected amino acid polymer or nucleic acid polymer when the position of any given polymer component (e.g., amino acid ...
  http://www.google.co.uk/patents/US7074590
*  A comparative study of conservation and variation scores | BMC Bioinformatics | Full Text
The cluster analysis showed that most scores fall into one of two groups--substitution matrix based group and frequency based ... introduced a score that focuses on the most common amino acid (α0) in each site, and sums over comparisons of each amino acid ... all scores in this cluster share the property that they consider individual amino acids rather than amino acid substitution as ... The scores marked with "w" as suffix in the score name in Table 3 use sequence weighting by the Henikoff-Henikoff method [9].. ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-388
*  Experimental Determination and Prediction of the Fitness Effects of Random Point Mutations in the Biosynthetic Enzyme HisA,...
... and BLOSUM amino acid substitution matrices (Grantham 1974; Dayhoff et al. 1978; Henikoff and Henikoff 1992) have previously ... The gene was introduced into the chromosome with λ red recombineering by counter selecting sacB. The fitness of each mutant was ... and BLOSUM amino acid substitution matrices (Grantham 1974; Dayhoff et al. 1978; Henikoff and Henikoff 1992) have previously ... Google Scholar CrossRef Search ADS Henikoff S , Henikoff JG. 1992. Amino acid substitution matrices from protein blocks. Proc ...
  https://www.deepdyve.com/lp/ou_press/experimental-determination-and-prediction-of-the-fitness-effects-of-nAPX9LV6TW
*  Defining Parameters for Homology-Tolerant Database Searching
Henikoff S, Henikoff JG. Amino acid matrices from protein blocks. Proc Natl Acad Sci USA 2003; 89:10915-10919. [PubMed] ... Allowing 30-50% amino acid substitution resulted in higher (p , .05) protein scores compared with limiting substitutions to 10 ... As the peptides are introduced, precursor ions are selected during an initial survey scan if their intensity is above a ... Blosum 62.18 Multiple peptide sequences may be submitted and searched simultaneously using MS-Homology. Therefore, to determine ...
  http://pubmedcentralcanada.ca/pmcc/articles/PMC2291706/
*  Sequence alignment - Wikipedia
Ng PC; Henikoff S (May 2001). "Predicting deleterious amino acid substitutions". Genome Res. 11 (5): 863-74. doi:10.1101/gr. ... Another common series of scoring matrices, known as BLOSUM (Blocks Substitution Matrix), encodes empirically derived ... introduced in one or both lineages in the time since they diverged from one another. In sequence alignments of proteins, the ... The absence of substitutions, or the presence of only very conservative substitutions (that is, the substitution of amino acids ...
  https://en.wikipedia.org/wiki/Sequence_alignment
*  Patent US6303749 - Agouti and agouti-related peptide analogs - Google Patents
Also provided are methods of preparing the peptides, as well as nucleic acid molecules encoding the peptides. ... For each amino acid, an additional conservative substitution includes the "homolog" of that amino acid, where the "homolog" is ... Comparison matrix: BLOSUM 62 from Henikoff and Henikoff, Proc. Natl. Acad. Sci. USA 89:10915-10919 (1992) ... Generally, a humanized antibody has one or more amino acid residues introduced into it from a source which is non-human. These ...
  http://www.google.com/patents/US6303749?dq=5787449
*  Optimizing substitution matrix choice and gap parameters for sequence alignment | BMC Bioinformatics | Full Text
BLOSUM matrices are found to be slightly inferior, even with the marginal improvements in the bug-fixed RBLOSUM series. The PAM ... It is also not well understood which substitution matrices are the most effective when alignment accuracy is the goal rather ... is described and applied to the problems of optimizing gap penalties and selecting substitution matrices for pair-wise global ... While substitution matrices can readily be computed from reference alignments, it is challenging to compute optimal or ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-396
*  Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases | BMC Bioinformatics | Full Text
Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. ProcNatlAcadSciUSA 1992, 89(22):10915-10919. ... Therefore, the BLOSUM model was used to provide substitution priors for the sequence partition of the data. A Metropolis- ... Manual adjustments were introduced into the alignments to preserve the continuity of secondary structure elements, either ... The tree based on features (Figure 9) generally agrees with the tree based solely on amino acid distances (Figure 8): in ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-73
*  Patent US7115368 - Diagnosis and treatment of cancer using mammalian pellino polypeptides and ... - Google Patents
... where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative ... and the BLOSUM 62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)) alignments (B) of 50, ... The particular procedure used to introduce the nucleic acids into a host cell for expression of a protein or nucleic acid is ... The term "amino acid" refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid ...
  http://www.google.com/patents/US7115368?dq=7222078
*  Combination Therapy with Co-Stimulatory Factors - Patent application
Amino acid changes encompass one or more amino acid substitutions in a CDR, ranging from a single amino acid difference to the ... 0094]Comparison matrix: BLOSUM 62 from Henikoff et al., supra (1992); [0095]Gap Penalty: 12 [0096]Gap Length Penalty: 4 [0097] ... In certain embodiments, amino acid changes may be introduced in selected regions of an antibody, such as in the light and/or ... conventional amino acids, unnatural amino acids such as α,α-disubstituted amino acids, N-alkyl amino acids, lactic acid, and ...
  http://www.patentsencyclopedia.com/app/20080279862
*  Virtual screening of GPCRs: An in silico chemogenomics approach | BMC Bioinformatics | Full Text
Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992, 89(22):10915-10919. ... could have introduced bias in the results. Such bias is certainly absent in the binding pocket kernel. The fact that the same ... with Blosum matrices [68]. Sequences which could not be correctly aligned (i.e. with important gaps in the transmembrane ... Amino acid side chains are represented for 6 of the 31 residues (in cyan, blue and red) of the binding pocket motif. ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-9-363
*  Indian Patents. 245529:A NEURAL THREAD PROTEIN (NTP) PEPTIDE
or more amino acid substitutions, deletions, and/or insertions are present. as compared to the amino acid sequence of an NTP ... Henikoff et al, Proc. Natl Acad. Sci USA, 89:10915-10919 [1992] for the. BLOSUM 62 comparison matrix) also may be used by the ... introducing cells, bacteria or viruses that express the peptide in vivo,. because of genetic modification or otherwise.. In ... sequence with a similar or homologous amino acid(s) or a dissimilar. amino acid(s). There are many scales on which amino acids ...
  http://www.allindianpatents.com/patents/245529-a-neural-thread-protein-ntp-peptide
*  Systemic administration of Hypocretin-1 - The Regents of the University of California
For amino acid alignments, the BLOSUM algorithm can be used as a protein weight matrix (Henikoff and Henikoff, 1992, Proc. Natl ... The effect of single amino acid substitutions can also be probed using D-amino acids. The number and types of residues which ... FECT was done by introducing a bowl of soft food (Pedigree, by Kalkan) in the home cage and counting the number of cataplectic ... propionic acid, glycolic acid, pyruvic acid, oxalic acid, malic acid, malonic acid, succinic acid, maleic acid, fumaric acid, ...
  http://www.freepatentsonline.com/7112566.html
*  GENE CAPABLE OF INCREASING THE PRODUCTION OF PLANT BIOMASS AND METHOD FOR USING THE SAME - Patent application
BLOSUM: Blocks of Amino Acid Substitution Matrix) is proposed in FIG. 2 of Reference (3): Henikoff S., Henikoff J. G., Amino- ... which comprises introducing a gene encoding a protein comprising a common sequence consisting of the amino acid sequence shown ... aspartic acid) and E (Glu, glutamic acid). 4) Basic Amino Acid (KR Group) [0054] This group is a group of basic amino acids, ... an amino acid residue denoted by "Xaa" in the amino acid sequence shown in SEQ ID NO: 1 is an arbitrary amino acid and is not ...
  http://www.patentsencyclopedia.com/app/20110239330
*  Indian Patents. 229347:CYTOKINE RECEPTOR ZALPHA11
... substitution frequencies can be used to define conservative amino acid substitutions that may be introduced into the amino acid ... "blosum 62" scoring matrix of Henikoff and Henikoff (ibid.) as shown in Table 3 (amino acids are indicated by the standard one- ... to amino acid number 255 (Leu);. (e) the amino acid sequence of SEQ ID N0:2 from amino acid number acid 238 (Leu) to amino acid ... a) the amino acid sequence of SEQ ID No.2 from amino acid number l(Met), to amino acid number 19 (Gly);. (b) the amino acid ...
  http://www.allindianpatents.com/patents/229347-cytokine-receptor-zalpha11
*  A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure | BMC...
Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 1992, 89: 10915-10919 ... Here, I introduce a dynamic programming solution to the problem of structural alignment of large RNAs. The central idea is a ... or BLOSUM [17] score matrices. Unlike specialized programs, a general alignment algorithm can be applied to find homologs of ... Needleman SB, Wunsch CD: A general method applicable to the search for similarities in the amino acid sequence of two proteins. ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-3-18
*  Compositions And Methods Involving Respiratory Syncytial Virus Subgroup B Strain 9320 - Patent application
For amino acid alignments, the BLOSUM algorithm can be used as a protein weight matrix. See, e.g., Henikoff and Henikoff (1992 ... to introduce, e.g., one or more nucleotide substitutions specifying one or more amino acid substitutions into an RSV ... an acetylated amino acid, an acylated amino acid, a PEG-ylated amino acid, a biotinylated amino acid, a carboxylated amino acid ... amino acid, addition of an amino acid, or substitution of an amino acid with a chemically similar amino acid. [0102] ...
  http://www.patentsencyclopedia.com/app/20120263744