Combining evolutionary information and neural networks to predict protein secondary structure

Proteins: Structure, Function, and Bioinformatics

Volumn 19, Issue 1, 1994, Pages 55-72

  Rost, Burkhard ^a   Sander, Chris ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

evolutionary information; multiple alignment profiles; prediction of secondary structure class; prediction of secondary structure content; secondary structure prediction

Indexed keywords

AMINO ACID COMPOSITION; AMINO ACID SEQUENCE; ARTICLE; CLONE; COMPUTER MODEL; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STATISTICAL ANALYSIS; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; EVOLUTION; NEURAL NETWORKS (COMPUTER); PROTEIN STRUCTURE, SECONDARY; SEQUENCE ALIGNMENT;

EID: 0028300741     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.340190108     Document Type: Article

References (135)

1. The SWISS‐PROT protein sequence data bank
2. The Protein Data Bank: A computer based archival file for macromolecular structure
3. Selection of representative protein data sets
4. The genetic control of tertiary protein structure: studies with model systems
5. Principles that govern the folding of protein chains
6. The relation between the divergence of sequence and structure in proteins
7. Protein structure alignment
8. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction
9. Modeling of globular proteins
10. Detection of common three‐dimensional substructures in proteins
11. Database of homology‐derived structures and the structural meaning of sequence alignment
12. Accurate modeling of protein conformation by automatic segment matching
13. Fast and simple Monte Carlo algorithm for side chain optimization in proteins: Application to model building by homology
14. New paths from dead ends
15. The HSSP data base of protein structure‐sequence alignment
16. Molecular dynamics simulations in biology
17. Molecular dynamics studies of proteins
18. Solvation energy in protein folding and binding
19. Polarity as a criterion in protein design
20. Prediction of protein folding from amino acid sequence over discrete conformation spaces
21. A search for the most stable folds of protein chains
22. Secondary structure‐based profiles: Use of structure‐conserving scoring tables in searching protein sequence databases for structural similarities
23. Assessment of protein models with three‐dimensional profiles
24. Environment‐specific amino acid substitution tables: Tertiary templates and prediction of protein folds
25. Prediction of protein structure by evaluation of sequence‐structure fitness: Aligning sequences to contact profiles derived from 3D structures
26. Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge‐based prediction of local structures of globular proteins
27. Detection of native‐like models for amino acid sequences of unknown three‐dimensional structure in a data base of known protein conformations
28. Configurations of polypeptide chains with favored orientations around single bonds: Two new pleated sheets
29. The structure of proteins: Two hydrogen‐bonded helical configurations of the polypeptide chain
30. Prediction of protein conformation
31. Prediction of the secondary structure of proteins from their amino acid sequence
32. Folding of polypeptide chains in proteins: A proposed mechanism for folding
33. Analysis of the code relating sequence to secondary structure in proteins
34. Analysis of the code relating sequence to conformation in proteins: Possible implications for the mechanism of formation of helical regions
35. Conformational properties of amino acid residues in globular proteins
36. Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins
37. Structural principles of the globular organization of protein chains. A stereochemical theory of globular protein secondary structure
38. Statistical analysis of the correlation among amino acid residues in helical, β‐structural and non‐regular regions of globular proteins
39. How good are predictions of protein secondary structure?
40. Hybrid system for protein secondary structure prediction
41. Predicting protein secondary structure with a nearest‐neighbor algorithm
42. Theory of protein secondary structure and algorithm of its prediction
43. Secondary structure prediction: Combination of three different methods
44. Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs
45. An algorithm for secondary structure determination in proteins based on sequence similarity
46. Improvements in a secondary structure prediction method based on a search for local sequence homologies and its use as a model building tool
47. A simple method for predicting the secondary structure of globular proteins: Implications and accuracy
48. New joint prediction algorithm (Q7‐JASEP) improves the prediction of protein secondary structure
49. Protein secondary structure prediction with a neural network
50. Predicting the secondary structure of globular proteins using neural network models
51. Prediction of structural and functional features of protein and nucleic acid sequences by artificial neural networks
52. The protein structure code: What is its present status?
53. Computer analysis of DNA and protein sequences
54. The cytochrome fold and the evolution of bacterial energy metabolism: J
55. Comparison of the structures of globing and phycocyanins: Evidence for evolutionary relationship
56. Improvements in the prediction of protein topography by reduction of statistical errors
57. Prediction of protein secondary structure and active sites using alignment of homologous sequences
58. Assessment of secondary structure prediction of proteins: Comparison of computerized Chou‐Fasman method with others
59. Predicted secondary structure for the Src homology 3 domain
60. Predicting de novo the folded structure of proteins
61. Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure of the catalytic domain of protein kinases
62. Amino acid sequence analysis of the annexin supergene family of proteins
63. Prediction of secondary structure by evolutionary comparison: Application to the α subunit of tryptophan synthase
64. DNA‐binding domain ancestry
65. Proposed structure for the DNA‐binding domain of the helix‐loop‐helix family of eukaryotic gene regulatory proteins
66. The nitrogenase MoFe protein
67. SH3—an abundant protein domain in search of a function
68. Conservation analysis and structure prediction of the SH2 family of phosphotyrosine binding domains
69. Jury returns on structure prediction
70. Improving the prediction of secondary structure of ‘TIM‐barrel’ enzymes (Corrigendum)
71. Improved prediction of protein secondary structure by use of sequence profiles and neural networks
72. Quantification of secondary structure prediction improvement using multiple alignments
73. Prediction of protein secondary structure at better than 70% accuracy
74. Progress in protein structure prediction?
75. Dictionary of Protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features
76. Learning representations by back‐propagating error
77. Analysis of insertions/deletions in protein structures
78. On the nature of‐the protein folding code
79. The local information content of the protein structural database
80. Predicting protein secondary structure content. A tandem neural network approach
81. Prediction of protein folding class from amino acid composition
82. An optimization approach to predicting protein structural class from amino acid composition
83. Cross‐validation of protein structural class prediction using statistical clustering and neural networks
84. Protein secondary structure and circular dichroism: A practical guide
85. Structural patterns in globular proteins
86. Classification of proteins into groups based on amino acid composition and other characters: I. Angular distribution
87. Correlation of the amino acid composition of a protein to its structural and biological characteristics
88. Improvements in protein secondary structure prediction by an enhanced neural network
89. Protein secondary structure prediction using logic‐based machine learning
90. Prediction of protein secondary structures by a neural network
91. Secondary structure assignment for α/β proteins by a combinatorial approach
92. Turn prediction in proteins using a pattern‐matching approach
93. Secondary structure prediction of all‐helical proteins in two states
94. Redefining the goals of protein secondary structure prediction
95. Protein secondary structure and homology by neural networks
96. PRONET: A microcomputer program for predicting the secondary structure of proteins with a neural network
97. Predicting secondary structures of membrane proteins with neural networks
98. Limits on α‐helix prediction with neural network models
99. γ
100. Structure of the PI3K SH3 domain and analysis of the SH3 family
101. The nonhelical structure of antifreeze protein type III
102. Analysis of the code relating sequence to conformation in globular proteins‐Theory and application of expected information
103. Prediction of protein structural class from the amino acid sequence
104. Prediction of protein function by discriminant analysis
105. Prediction of protein structural class by discriminant analysis
106. An algorithm for protein secondary structure prediction based on class prediction
107. Amino acid composition and hydrophobicity patterns of protein domains correlate with their structures
108. Prediction of protein backbone conformation based on seven structure assignments: Influence of local interactions
109. Extracting information on folding from the amino acid sequence: Accurate predictions for protein regions with preferred conformation in the absence of tertiary interactions
110. Extracting information on folding from the amino acid sequence: Consensus regions with preferred conformation in homologous proteins
111. Crystal structure of a flavoprotein related to the subunits of bacterial luciferase
112. One thousand protein families for the molecular biologist
113. Search for the stable state of a short chain in a molecular field
114. Physical reasons for secondary structure stability: α‐Helices in short peptides
115. Comparison of the predicted and observed secondary structure of T4 phage lysozyme
116. Predicting the conformation of proteins: Man versus machine
117. Correct structure prediction?
118. Crystal structure of the catalytic subunit of cyclic adenosine monophosphate‐dependent protein kinase
119. Solution structure of the SH3 domain of Src and identification of its ligand‐binding site
120. Crystal structure of a Src‐homology 3 (SH3) domain
121. Crystallographic structure and functional implications of the nitrogenase molybdenum‐iron protein from Azotobacter vinelandii
122. Convex constraint analysis: A natural deconvolution of circular dichroism curves of proteins
123. Deconvolution of the circular dichroism spectra of proteins: The circular dichroism spectra of the antiparallel β‐sheet in proteins
124. Quantitative analysis of protein far UV circular dichroism spectra by neural networks
125. Evaluation of secondary structure of proteins from UV circular dichroism spectra using an unsupervised learning neural network