Comparison of two optimization methods to derive energy parameters for protein folding: Perceptron and Z score

Proteins: Structure, Function and Genetics

Volumn 41, Issue 2, 2000, Pages 192-201

  Vendruscolo, Michele ^a   Mirny, Leonid A ^b   Shakhnovich, Eugene I ^b   Domany, Eytan ^c  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b HARVARD UNIVERSITY   (United States)

^c WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

Contact maps; Perceptron; Protein folding; Protein potential; Z score

Indexed keywords

ANALYTICAL PARAMETERS; ARTICLE; CONFORMATION; ENERGY; INTERMETHOD COMPARISON; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; SYSTEM ANALYSIS;

ALGORITHMS; NEURAL NETWORKS (COMPUTER); PROTEIN FOLDING; THERMODYNAMICS;

EID: 0034332976     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/1097-0134(20001101)41:2<192::AID-PROT40>3.0.CO;2-3     Document Type: Article

References (23)

1. Pairwise contact potentials are unsuitable for protein folding
2. Optimal protein-folding codes from spin-glass theory
3. Protein tertiary structure recognition using optimized Hamiltonians with local interactions
4. Prediction of protein folding from amino-acid-sequence over discrete conformation spaces
5. Contact potential that recognizes the correct folding of globular proteins
6. Easily searched protein folding potentials
7. How optimization of potential function affects protein folding
8. Extraction of interaction potentials between amino acids from native protein structures
9. Proc Natl Acad Sci USA
10. How to derive a protein folding potential? A new approach to an old problem
11. Equation of state calculations by fast computing machines
12. Learning algorithms with optimal stability in neural networks
13. Can a pairwise contact potential stabilize native protein folds against decoys obtained by threading?
14. Estimation of effective inter-residue contact energies from protein crystal structures: Quasi-chemical approximation
15. Engineering of stable and fast-folding sequences of model proteins
16. A novel approach to design of stable proteins
17. Protein folding in contact map space
18. Protein structure prediction by threading. When it works and when it does not
19. Salt bridge stability in monomeric proteins
20. Protein binding versus protein folding: The role of hydrophilic bridges
21. How do potentials derived from structural databases relate to 'true' potentials?