Comparative protein structure modeling of genes and genomes
MA Martí-Renom, AC Stuart, A Fiser… - Annual review of …, 2000 - annualreviews.org
▪ Abstract Comparative modeling predicts the three-dimensional structure of a given protein
sequence (target) based primarily on its alignment to one or more proteins of known …
sequence (target) based primarily on its alignment to one or more proteins of known …
Three-dimensional protein structure prediction: Methods and computational strategies
A long standing problem in structural bioinformatics is to determine the three-dimensional (3-
D) structure of a protein when only a sequence of amino acid residues is given. Many …
D) structure of a protein when only a sequence of amino acid residues is given. Many …
Predicting functions from protein sequences—where are the bottlenecks?
The exponential growth of sequence data does not necessarily lead to an increase in
knowledge about the functions of genes and their products. Prediction of function using …
knowledge about the functions of genes and their products. Prediction of function using …
[图书][B] Handbook of computational molecular biology
S Aluru - 2005 - taylorfrancis.com
The enormous complexity of biological systems at the molecular level must be answered
with powerful computational methods. Computational biology is a young field, but has seen …
with powerful computational methods. Computational biology is a young field, but has seen …
Protein threading using PROSPECT: design and evaluation
The computer system PROSPECT for the protein fold recognition using the threading
method is described and evaluated in this article. For a given target protein sequence and a …
method is described and evaluated in this article. For a given target protein sequence and a …
Alignment of protein sequences by their profiles
MA Marti‐Renom, MS Madhusudhan, A Sali - Protein Science, 2004 - Wiley Online Library
The accuracy of an alignment between two protein sequences can be improved by including
other detectably related sequences in the comparison. We optimize and benchmark such an …
other detectably related sequences in the comparison. We optimize and benchmark such an …
Distribution of protein folds in the three superkingdoms of life
YI Wolf, SE Brenner, PA Bash, EV Koonin - Genome research, 1999 - genome.cshlp.org
A sensitive protein-fold recognition procedure was developed on the basis of iterative
database search using the PSI-BLAST program. A collection of 1193 position-dependent …
database search using the PSI-BLAST program. A collection of 1193 position-dependent …
Protein fold recognition using sequence profiles and its application in structural genomics
246 EUGENE V. KOONIN ET AL. 50% of the globular proteins encoded in each of the
bacterial and archaeal genomes. The lists of top-ranking folds are similar in bacteria and …
bacterial and archaeal genomes. The lists of top-ranking folds are similar in bacteria and …
Computational tools for protein modeling
Protein modeling is playing a more and more important role in protein and peptide sciences
due to improvements in modeling methods, advances in computer technology, and the huge …
due to improvements in modeling methods, advances in computer technology, and the huge …
In silico identification, structure prediction and phylogenetic analysis of the 2′-O-ribose (cap 1) methyltransferase domain in the large structural protein of ssRNA …
JM Bujnicki, L Rychlewski - Protein engineering, 2002 - academic.oup.com
Abstract The Escherichia coli RrmJ gene product has recently been shown to be the 23S
rRNA: U2552 specific 2′-O-ribose methyltransferase (MTase)(RrmJ). Its structure has been …
rRNA: U2552 specific 2′-O-ribose methyltransferase (MTase)(RrmJ). Its structure has been …