protein secondary structure prediction; multiple sequence alignments; secondary structure content; neural network 1. Introduction Large-scale sequencing projects produce an exploding number of known protein sequences. The current number is 26,000 (BaJroch & Boeckmann, 1992) sequences, but before the end of the century 100,000 will have to be dealt with. This is in contrast to the much slower increase in the number of known protein structures, currently at about 1000 (Bernstein eI a!., 1977}. Can theory help to narrow the widening gap? The most reliable prediction of the structure of new proteins is done by detection of significant similarities to proteins of known structure (Taylor & Orengo, 1989; Saander & Schneider, 1991; Vriend & Sander, 1991). But only about one-seventh of new sequences have sequence similarities to known structures (Bork et al., 1992). What about the restS. Attempts to predict structure from sequence by physical simulation techniques such as
|
1405
|
Introduction to the Theory of Neural Computation
– Hertz, Krogh, et al.
- 1991
|
|
485
|
Learning representations by back-propagating errors
– Rumelhart, Hinton, et al.
- 1986
|
|
460
|
C: Dictionary of Protein Secondary Structure – Pattern-Recognition of Hydrogen-Bonded and Geometrical Features. Biopolymers
– Kabsch, Sander
- 1983
|
|
370
|
Neural network ensembles
– Hansen, Salamon
- 1990
|
|
319
|
The Swiss-Prot Protein Sequence Data Bank User Manual. Release 35
– Bairoch
- 1997
|
|
256
|
The protein data bank: A computer-based archival file for macromolecular structures
– Bernstein, Koetzle, et al.
- 1977
|
|
152
|
Predicting the Secondary Structure of Globular Proteins Using Neural Networks. J.Mol. Biol
– Qian, Sejnowski
- 1988
|
|
122
|
BW: Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim Biophys Acta 1975, 405(2):442-451. Publish with BioMed Central and every scientist can read your work free of charge "BioMed Central will be the most significan
– Matthews
|
|
60
|
Chothia C: Structural patterns in globular proteins. Nature
– Levitt
- 1976
|
|
60
|
A hybrid system for protein secondary structure prediction
– Zhang, Mersirov, et al.
- 1992
|
|
46
|
Selection of representative protein data sets. Protein Sci
– Hobohm, Scharf, et al.
- 1992
|
|
42
|
Karplus M: Protein secondary structure prediction with a neural network
– LH
- 1989
|
|
32
|
Prediction of protein conformation
– Chou, Fasman
- 1974
|
|
29
|
Improvements in protein secondary structure prediction by an enhanced neural network
– Kneller, Cohen, et al.
- 1990
|
|
29
|
Detection of common three-dimensional substructures in proteins. Proteins: Struct
– Vriend, Sander
- 1991
|
|
27
|
Further developments of protein secondary structure prediction using information theory
– Gibrat, Garnier, et al.
- 1987
|
|
27
|
The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide
– Pauling, Corey, et al.
- 1951
|
|
15
|
Molecular dynamics simulations in biology
– Karplus, Petsko
- 1990
|
|
15
|
Gamier J: An algorithm for secondary structure determination in proteins based on sequence similarity
– JM, Robson
- 1986
|
|
12
|
Configurations of polypeptide chains with favoured orientations around single bonds: Two new pleated sheets
– Pauling, Corey
- 1951
|
|
11
|
Protein secondary structure and homology by neural networks
– Bohr
- 1988
|
|
11
|
Structural Principles of the Globular Organization of Protein Chains. A Stereochemical Theory of Globular Protein Secondary Structure
– Lim
- 1974
|
|
11
|
S-H: Predicting protein secondary structure content: a tandem neural network approach
– SM, Kim
- 1992
|
|
10
|
A Novel Approach to prediction of the 3-dimensional structures of protein backbones by neural networks
– Bohr, Bohr, et al.
- 1990
|
|
9
|
Improvements in a secondary structure prediction method based on a search for local sequence homologies and its use as a model building tool
– Levin, Garnier
- 1988
|
|
9
|
Secondary structure prediction of all-helical proteins in two states
– Rost, Sander
- 1993
|
|
8
|
Turn prediction in proteins using a pattern-matching approach
– Cohen, Abarbanel, et al.
- 1986
|
|
8
|
Predicting protein secondary structure with a nearest-neighbor algorithm
– Salzberg, Cost
- 1992
|
|
7
|
The genetic control of tertiary protein structure: studies with model systems
– Epstein, Goldberger, et al.
- 1963
|
|
7
|
Numerical Recipes: The Art of Scientific Computing
– H
- 1986
|
|
7
|
Pattern matching methods in protein sequence comparison and structure prediction
– Taylor
- 1988
|
|
6
|
Neural Networks: The Early Days
– Cowan
- 1990
|
|
6
|
A segment-based approach to protein secondary structure prediction
– Presnell, Cohen, et al.
- 1992
|
|
5
|
Amino acid sequence analysis of the annexin super-gene family of proteins
– Barton, Newman, et al.
- 1991
|
|
5
|
Protein secondary structure and circular dichroism: a practical guide
– Johnson
- 1990
|
|
5
|
Predicting protein secondary structure based on amino acid sequence
– Nishikawa, Noguchi
- 1991
|
|
5
|
Jury returns on structure prediction
– Rost, Sander
- 1992
|
|
5
|
Conservation analysis and structure prediction of the SH2 family of phosphotyrosine binding domains
– Russell, Breed, et al.
- 1992
|
|
4
|
Tertiary structure prediction
– Cohen, Kuntz
- 1989
|
|
4
|
A multivariate analysis method for discriminating protein secondary structural segments, Protein Eng
– Kanehisa
- 1988
|
|
3
|
PRONET: a microcomputer program for predicting the secondary structure of proteins with a neural network
– Bossa
- 1990
|
|
3
|
DNA-binding domain ancestry
– Frampton, Leutz, et al.
- 1989
|
|
3
|
Improvements in the prediction of protein topography by reduction of statistical errors
– Maxfield, Scheraga
- 1979
|
|
3
|
SH3 - an abundant protein domain in search ,>f a function
– Musacchio, Gibson, et al.
- 1992
|
|
3
|
A holistic approach to protein structure alignment
– Taylor, Orengo
- 1989
|
|
2
|
Modeling Brain Function: The World of Attractor Networks
– Amir
- 1989
|
|
2
|
What's in a genome
– Bork, Ouzonis, et al.
- 1992
|
|
2
|
Protein folding by stages
– Ewbank
- 1992
|
|
2
|
Proposed structure for the DNA-binding domain of the helix-loop-helix family of eukaryotic gene regulatory proteins. Protein Eng
– Gibson, Thompson
- 1993
|
|
2
|
The role of heatshock and chaperone proteins in protein folding: possible molecular mechanisms. Protein Eng
– Hubbard
- 1991
|
