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Literature DB >> 8876187

An iterative method for extracting energy-like quantities from protein structures.

Abstract

We present a method (ENERGI) for extracting energy-like quantities from a data base of protein structures. In this paper, we use the method to generate pairwise additive amino acid "energy" scores. These scores are obtained by iteration until they correctly discriminate a set of known protein folds from decoy conformations. The method succeeds in lattice model tests and in the gapless threading problem as defined by Maiorov and Crippen [Maiorov, V. N. & Crippen, G. M. (1992) J. Mol. Biol. 227, 876-888]. A more challenging test of threading a larger set of test proteins derived from the representative set of Hobohm and Sander [Hobohm, U. & Sander, C. (1994) Protein Sci. 3, 522-524] is used as a "workbench" for exploring how the ENERGI scores depend on their parameter sets.

Mesh：

Substances：
Amino Acids
Proteins

Year: 1996 PMID： 8876187 PMCID： PMC38109 DOI： 10.1073/pnas.93.21.11628

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

31 in total

1. Contact potential that recognizes the correct folding of globular proteins.

Authors: V N Maiorov; G M Crippen
Journal: J Mol Biol Date: 1992-10-05 Impact factor: 5.469

Review 2. Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds.

Authors: G Casari; M J Sippl
Journal: J Mol Biol Date: 1992-04-05 Impact factor: 5.469

3. Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations.

Authors: M J Sippl; S Weitckus
Journal: Proteins Date: 1992-07

An iterative method for extracting energy-like quantities from protein structures.

1. Contact potential that recognizes the correct folding of globular proteins.

Review 2. Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds.

3. Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations.

4. Simulations of the folding of a globular protein.

Review 5. Structure-derived potentials and protein simulations.

6. Computer modeling of protein folding: conformational and energetic analysis of reduced and detailed protein models.

7. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme.

8. Statistical potentials extracted from protein structures: how accurate are they?

9. Global optimum protein threading with gapped alignment and empirical pair score functions.

10. An empirical energy function for threading protein sequence through the folding motif.

1. A statistical mechanical method to optimize energy functions for protein folding.

2. A method for parameter optimization in computational biology.

3. Determination of domain structure of proteins from X-ray solution scattering.

4. Computer simulations of membrane protein folding: structure and dynamics.

5. An optimal structure-discriminative amino acid index for protein fold recognition.

6. Addition of missing loops and domains to protein models by x-ray solution scattering.

7. Recovering physical potentials from a model protein databank.

8. Scoring and lessons learned with the CSAR benchmark using an improved iterative knowledge-based scoring function.

9. Inferring ideal amino acid interaction forms from statistical protein contact potentials.

10. Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions.