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NAR
2007
91views more  NAR 2007»
8 years 8 months ago
RNABindR: a server for analyzing and predicting RNA-binding sites in proteins
Understanding interactions between proteins and RNA is key to deciphering the mechanisms of many important biological processes. Here we describe RNABindR, a web-based server that...
Michael Terribilini, Jeffry D. Sander, Jae-Hyung L...
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
2004
125views more  BMCBI 2004»
8 years 9 months ago
A fast algorithm for determining the best combination of local alignments to a query sequence
Background: Existing sequence alignment algorithms assume that similarities between DNA or amino acid sequences are linearly ordered. That is, stretches of similar nucleotides or ...
Gavin C. Conant, Andreas Wagner
BMCBI
2004
85views more  BMCBI 2004»
8 years 9 months ago
Frequent occurrence of recognition Site-like sequences in the restriction endonucleases
Background: There are two different theories about the development of the genetic code. Woese suggested that it was developed in connection with the amino acid repertoire, while C...
Jan C. Biro, Josephine M. K. Biro
JCC
2007
82views more  JCC 2007»
8 years 9 months ago
Peptide reagent design based on physical and chemical properties of amino acid residues
: It has tremendous values for both drug discovery and basic research to develop a solid bioinformatical tool for guiding peptide reagent design. Based on the physical and chemical...
Qishi Du, Ri-Bo Huang, Yu-Tuo Wei, Cheng-Hua Wang,...
BMCBI
2005
118views more  BMCBI 2005»
8 years 9 months ago
Variation in structural location and amino acid conservation of functional sites in protein domain families
Background: The functional sites of a protein present important information for determining its cellular function and are fundamental in drug design. Accordingly, accurate methods...
Birgit Pils, Richard R. Copley, Jörg Schultz
BMCBI
2005
106views more  BMCBI 2005»
8 years 9 months ago
SIMPROT: Using an empirically determined indel distribution in simulations of protein evolution
Background: General protein evolution models help determine the baseline expectations for the evolution of sequences, and they have been extensively useful in sequence analysis an...
Andy Pang, Andrew D. Smith, Paulo A. S. Nuin, Elis...
BMCBI
2005
138views more  BMCBI 2005»
8 years 9 months ago
Detailed protein sequence alignment based on Spectral Similarity Score (SSS)
Background: The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine ali...
Kshitiz Gupta, Dina Thomas, S. V. Vidya, K. V. Ven...
BMCBI
2005
90views more  BMCBI 2005»
8 years 9 months ago
TMB-Hunt: An amino acid composition based method to screen proteomes for beta-barrel transmembrane proteins
Background: Beta-barrel transmembrane (bbtm) proteins are a functionally important and diverse group of proteins expressed in the outer membranes of bacteria (both gram negative a...
Andrew G. Garrow, Alison Agnew, David R. Westhead
BMCBI
2005
91views more  BMCBI 2005»
8 years 9 months ago
COPASAAR - A database for proteomic analysis of single amino acid repeats
Background: Single amino acid repeats make up a significant proportion in all of the proteomes that have currently been determined. They have been shown to be functionally and med...
Daniel P. Depledge, Andrew R. Dalby
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