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CORR
2002
Springer
110views Education» more  CORR 2002»
8 years 9 months ago
Long Proteins with Unique Optimal Foldings in the H-P Model
It is widely accepted that (1) the natural or folded state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state determined by their amino ...
Oswin Aichholzer, David Bremner, Erik D. Demaine, ...
BMCBI
2005
125views more  BMCBI 2005»
8 years 9 months ago
Multiple sequence alignments of partially coding nucleic acid sequences
Background: High quality sequence alignments of RNA and DNA sequences are an important prerequisite for the comparative analysis of genomic sequence data. Nucleic acid sequences, ...
Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried,...
BMCBI
2006
101views more  BMCBI 2006»
8 years 9 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
100views more  BMCBI 2006»
8 years 9 months ago
STAR: predicting recombination sites from amino acid sequence
Background: Designing novel proteins with site-directed recombination has enormous prospects. By locating effective recombination sites for swapping sequence parts, the probabilit...
Denis C. Bauer, Mikael Bodén, Ricarda Thier...
BMCBI
2006
89views more  BMCBI 2006»
8 years 9 months ago
ORENZA: a web resource for studying ORphan ENZyme activities
Background: Despite the current availability of several hundreds of thousands of amino acid sequences, more than 36% of the enzyme activities (EC numbers) defined by the Nomenclat...
Olivier Lespinet, Bernard Labedan
BMCBI
2007
144views more  BMCBI 2007»
8 years 9 months ago
Application of amino acid occurrence for discriminating different folding types of globular proteins
Background: Predicting the three-dimensional structure of a protein from its amino acid sequence is a long-standing goal in computational/molecular biology. The discrimination of ...
Y.-h. Taguchi, M. Michael Gromiha
BMCBI
2008
130views more  BMCBI 2008»
8 years 9 months ago
A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm
Background: The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence ...
Sheila Podell, Terry Gaasterland, Eric E. Allen
BMCBI
2008
114views more  BMCBI 2008»
8 years 9 months ago
Combining classifiers for improved classification of proteins from sequence or structure
Background: Predicting a protein's structural or functional class from its amino acid sequence or structure is a fundamental problem in computational biology. Recently, there...
Iain Melvin, Jason Weston, Christina S. Leslie, Wi...
BMCBI
2010
72views more  BMCBI 2010»
8 years 9 months ago
Potentials 'R'Us web-server for protein energy estimations with coarse-grained knowledge-based potentials
Background: Knowledge-based potentials have been widely used in the last 20 years for fold recognition, protein structure prediction from amino acid sequence, ligand binding, prot...
Yaping Feng, Andrzej Kloczkowski, Robert L. Jernig...
HICSS
1994
IEEE
157views Biometrics» more  HICSS 1994»
9 years 1 months ago
A Protein Family Classification Method for Analysis of Large DNA Sequences
A method is described for identification and classification of proteins encoded in large DNA sequences. Previously, an automated system was introduced for the general detection of...
Steven Henikoff, Jorja G. Henikoff
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