Results 1 to 10 of about 2,634,502 (395)

An Alternative Model of Amino Acid Replacement [PDF]

Bioinformatics 2005 21(7):975-980, 2004
The observed correlations between pairs of homologous protein sequences are typically explained in terms of a Markovian dynamic of amino acid substitution. This model assumes that every location on the protein sequence has the same background distribution of amino acids, an assumption that is incompatible with the observed heterogeneity of protein ...
Altschul, Altschul, Bennet, Brenner, Brenner, Bruno, Crooks, Crooks, Felsenstein, Goldman, Goldman, Gonnet, Henikoff, Henikoff, Jones, Koshi, Marti-Renom, Muller, Murzin, M  ller, Park, Schneider, Sjolander, Smith, Thorne, Topham, Yona, Zachariah   +27 more
arxiv   +5 more sources

Amino acid metabolism conflicts with protein diversity [PDF]

arXiv, 2014
The twenty protein coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid metabolic costs differ similarly, constraining their incorporation into proteins.
Alonso, Leonardo G., Ferreiro, Diego U., Krick, Teresa, Sanchez, Ignacio E., Shub, David A., Shub, Michael, Verstraete, Nina   +6 more
arxiv   +7 more sources

Predicting the functional effect of amino acid substitutions and indels. [PDF]

PLoS ONE, 2012
As next-generation sequencing projects generate massive genome-wide sequence variation data, bioinformatics tools are being developed to provide computational predictions on the functional effects of sequence variations and narrow down the search of ...
Yongwook Choi, Gregory E Sims, Sean Murphy, Jason R Miller, Agnes P Chan   +4 more
doaj   +2 more sources

OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs [PDF]

Bioinformatics 35 (17) 2974--2981 (2019), 2018
Motivation: High-throughput sequencing of large immune repertoires has enabled the development of methods to predict the probability of generation by V(D)J recombination of T- and B-cell receptors of any specific nucleotide sequence. These generation probabilities are very non-homogeneous, ranging over 20 orders of magnitude in real repertoires.
Zachary M. Sethna, Yuval Elhanati, Jr Curtis G. Callan, A. Walczak, T. Mora   +4 more
arxiv   +3 more sources

Amino acid classification based spectrum kernel fusion for protein subnuclear localization [PDF]

BMC Bioinformatics, 2010
Background Prediction of protein localization in subnuclear organelles is more challenging than general protein subcelluar localization. There are only three computational models for protein subnuclear localization thus far, to the best of our knowledge.
Fei Wang, Mei Suyu
doaj   +4 more sources

SSE: a nucleotide and amino acid sequence analysis platform

BMC Research Notes, 2012
Background There is an increasing need to develop bioinformatic tools to organise and analyse the rapidly growing amount of nucleotide and amino acid sequence data in organisms ranging from viruses to eukaryotes.
Simmonds Peter
doaj   +2 more sources

Organizing the bacterial annotation space with amino acid sequence embeddings [PDF]

BMC Bioinformatics, 2022
Background Due to the ever-expanding gap between the number of proteins being discovered and their functional characterization, protein function inference remains a fundamental challenge in computational biology.
Susanna R. Grigson, Jody C. McKerral, James G. Mitchell, Robert A. Edwards   +3 more
doaj   +2 more sources

Reading the three-dimensional structure of a protein from its amino acid sequence [PDF]

arXiv, 2000
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of a protein whose sequence is known. This situation is not particularly satisfactory, in keeping with the fact that
Broglia, R. A., Tiana, G.
arxiv   +3 more sources

THE AMINO ACID SEQUENCE OF HYPERTENSIN II [PDF]

The Journal of Experimental Medicine, 1956
The amino acid sequence of horse hypertensin II has been determined by the use of chymotrypsin, the fluorodinitrobenzene method, and stepwise phenylisothiocyanate degradation. The results indicate that the amino acids of hypertensin II are arranged in the following order: asp-arg-val-tyr-iso-hist-pro-phe.
Leonard T. Skeggs, Kenneth E. Lentz, Joseph R. Kahn, Norman P. Shumway, Kenneth R. Woods   +4 more
openalex   +5 more sources

The Amino Acid Sequence of Ribonuclease T1 [PDF]

Journal of Biological Chemistry, 1965
into other products. Glucoand galactocerebrosides, and ceramide trisaccharide, showed no activity (i.e. less than 300 cpm soluble in chloroform-methanol). Chloroform-methanolsoluble products were obtained with the following lipids: 4900 cpm with hematoside at 0.1 pmole per incubation mixture, and 7900 at 0.2 pmole; ceramide disaccharide, 720 cpm at 0.1
Kenji Takahashi
openalex   +3 more sources