108views more  IJBRA 2010»
13 years 1 months ago
Assessing and improving the accuracy of detecting protein adaptation with the TreeSAAP analytical software
The TreeSAAP software has been successfully used in a variety of protein studies for identifying and characterizing adaptation in terms of shifts in the physicochemical properties ...
David A. McClellan, David D. Ellison
147views Hardware» more  ICCAD 2009»
13 years 2 months ago
SAT-based protein design
Computational protein design can be formulated as an optimization problem, where the objective is to identify the sequence of amino acids that minimizes the energy of a given prot...
Noah Ollikainen, Ellen Sentovich, Carlos Coelho, A...
87views more  PAMI 1998»
13 years 3 months ago
Learning Local Languages and Their Application to DNA Sequence Analysis
—This paper concerns an efficient algorithm for learning in the limit a special type of regular languages called strictly locally testable languages from positive data, and its a...
Takashi Yokomori, Satoshi Kobayashi
112views more  NAR 2000»
13 years 4 months ago
ExInt: an Exon/Intron database
The Exon/Intron (ExInt) database incorporates information on the exon/intron structure of eukaryotic genes. Features in the database include: intron nucleotide sequence, amino aci...
Meena K. Sakharkar, Manyuan Long, Tin Wee Tan, San...
123views more  NAR 2000»
13 years 4 months ago
Update of AMmtDB: a database of multi-aligned Metazoa mitochondrial DNA sequences
The AMmtDB database ( srs6/ ) has been updated by collecting the multi-aligned sequences of Chordata mitochondrial genes coding for proteins and tRNA...
Cecilia Lanave, Sabino Liuni, Flavio Licciulli, Ma...
108views more  NAR 2000»
13 years 4 months ago
AAindex: Amino Acid index database
AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. It consists of two sections: AA...
Shuichi Kawashima, Minoru Kanehisa
265views more  BMCBI 2004»
13 years 4 months ago
ASAView: Database and tool for solvent accessibility representation in proteins
Background: Accessible surface area (ASA) or solvent accessibility of amino acids in a protein has important implications. Knowledge of surface residues helps in locating potentia...
Shandar Ahmad, M. Michael Gromiha, Hamed Fawareh, ...
168views more  MAGS 2007»
13 years 4 months ago
Agent-based protein structure prediction
A protein is identified by a finite sequence of amino acids, each of them chosen from a set of 20 elements. The Protein Structure Prediction Problem is the problem of predicting...
Luca Bortolussi, Agostino Dovier, Federico Fogolar...
120views more  BMCBI 2005»
13 years 4 months ago
pSLIP: SVM based protein subcellular localization prediction using multiple physicochemical properties
Background: Protein subcellular localization is an important determinant of protein function and hence, reliable methods for prediction of localization are needed. A number of pre...
Deepak Sarda, Gek Huey Chua, Kuo-Bin Li, Arun Kris...
132views more  BMCBI 2005»
13 years 4 months ago
Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein
Background: A large number of papers have been published on analysis of microarray data with particular emphasis on normalization of data, detection of differentially expressed ge...
Gajendra P. S. Raghava, Joon H. Han