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JCC
2006
67views more  JCC 2006»
10 years 2 months ago
Heuristic molecular lipophilicity potential (HMLP): Lipophilicity and hydrophilicity of amino acid side chains
: Heuristic molecular lipophilicity potential (HMLP) is applied in the study of lipophilicity and hydrphilcity of 20 natural amino acids side chains. The HMLP parameters, surface a...
Qishi Du, Da-Peng Li, Wen-Zhang He, Kuo-Chen Chou
BMCBI
2006
101views more  BMCBI 2006»
10 years 2 months ago
Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives
Background: Predicting residues' contacts using primary amino acid sequence alone is an important task that can guide 3D structure modeling and can verify the quality of the ...
Petras J. Kundrotas, Emil Alexov
BMCBI
2006
112views more  BMCBI 2006»
10 years 2 months ago
Protein disorder prediction by condensed PSSM considering propensity for order or disorder
Background: More and more disordered regions have been discovered in protein sequences, and many of them are found to be functionally significant. Previous studies reveal that dis...
Chung-Tsai Su, Chien-Yu Chen, Yu-Yen Ou
BMCBI
2006
60views more  BMCBI 2006»
10 years 2 months ago
Use of a multi-way method to analyze the amino acid composition of a conserved group of orthologous proteins in prokaryotes
Background: Amino acids in proteins are not used equally. Some of the differences in the amino acid composition of proteins are between species (mainly due to nucleotide compositi...
Alberto Pasamontes, Santiago Garcia-Vallvé
BMCBI
2007
106views more  BMCBI 2007»
10 years 2 months ago
Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach
Background: Selenocysteine and pyrrolysine are the 21st and 22nd amino acids, which are genetically encoded by stop codons. Since a number of microbial genomes have been completel...
Masashi Fujita, Hisaaki Mihara, Susumu Goto, Nobuy...
BMCBI
2010
138views more  BMCBI 2010»
10 years 2 months ago
A model-independent approach to infer hierarchical codon substitution dynamics
Background: Codon substitution constitutes a fundamental process in molecular biology that has been studied extensively. However, prior studies rely on various assumptions, e.g. r...
Olof Görnerup, Martin Nilsson Jacobi
BMCBI
2010
130views more  BMCBI 2010»
10 years 2 months ago
Amino acid "little Big Bang": Representing amino acid substitution matrices as dot products of Euclidian vectors
Background: Sequence comparisons make use of a one-letter representation for amino acids, the necessary quantitative information being supplied by the substitution matrices. This ...
Karel Zimmermann, Jean-François Gibrat
ALMOB
2007
155views more  ALMOB 2007»
10 years 2 months ago
Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid rep
Background: Some amino acid residues functionally interact with each other. This interaction will result in an evolutionary co-variation between these residues – coevolution. Ou...
Rodrigo Gouveia-Oliveira, Anders Gorm Pedersen
ISMB
1997
10 years 4 months ago
ANOLEA: A WWW Server to Assess Protein Structures
ANOLEA (Atomic Non-Local Environment Assessment) is a www server that performs energy calculations at the atomic level in protein structures. The calculations involve the non-loca...
Francisco Melo, Damien Devos, Eric Depiereux, Erne...
METMBS
2003
128views Mathematics» more  METMBS 2003»
10 years 4 months ago
Genetic Code as a Gray Code Revisited
In this paper we revisit the idea of relating the genetic code to a Gray code. This idea was originally fostered by Rosemary Swanson as a “unifying concept for the amino acid co...
Dragan Bosnacki, Huub M. M. ten Eikelder, Peter A....
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