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Literature DB >> 9491348

Comparison of protein surfaces using a genetic algorithm.

A R Poirrette¹, P J Artymiuk, D W Rice, P Willett.

Abstract

A genetic algorithm (GA) is described which is used to compare the solvent-accessible surfaces of two proteins or fragments of proteins, represented by a dot surface calculated using the Connolly algorithm. The GA is used to move one surface relative to the other to locate the most similar surface region between the two. The matching process is enhanced by the use of the surface normals and shape terms provided by the Connolly program and also by a simple hydrogen-bonding descriptor and an additional shape descriptor. The algorithm has been tested in applications ranging from the comparison of small surface patches to the comparison of whole protein surfaces, and it has performed correctly in all cases. Examples of the matches are given and a quantitative analysis of the quality of the matches is performed. A number of possible future enhancements to the program are described which would allow the GA to be used for more complex surface comparisons.

Entities: Chemical

Mesh：

Substances：

Year: 1997 PMID： 9491348 DOI： 10.1023/a:1007966011516

Source DB: PubMed Journal: J Comput Aided Mol Des ISSN： 0920-654X Impact factor: 3.686

39 in total

1. A new tool for the qualitative and quantitative analysis of protein surfaces using B-spline and density of surface neighborhood.

Authors: N Colloc'h; J P Mornon
Journal: J Mol Graph Date: 1990-09

2. Crystallographic refinement of the three-dimensional structure of the FabD1.3-lysozyme complex at 2.5-A resolution.

Authors: T O Fischmann; G A Bentley; T N Bhat; G Boulot; R A Mariuzza; S E Phillips; D Tello; R J Poljak
Journal: J Biol Chem Date: 1991-07-15 Impact factor: 5.157

3. Protein clefts in molecular recognition and function.

Authors: R A Laskowski; N M Luscombe; M B Swindells; J M Thornton
Journal: Protein Sci Date: 1996-12 Impact factor: 6.725

4. Molecular surface-volume and property matching to superpose flexible dissimilar molecules.

Authors: T D Perkins; J E Mills; P M Dean
Journal: J Comput Aided Mol Des Date: 1995-12 Impact factor: 3.686

5. Molecular skins: a new concept for quantitative shape matching of a protein with its small molecule mimics.

Authors: B B Masek; A Merchant; J B Matthew
Journal: Proteins Date: 1993-10

6. Structure of myoglobin refined at 2-0 A resolution. II. Structure of deoxymyoglobin from sperm whale.

Authors: T Takano
Journal: J Mol Biol Date: 1977-03-05 Impact factor: 5.469

7. Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm.

Authors: H M Grindley; P J Artymiuk; D W Rice; P Willett
Journal: J Mol Biol Date: 1993-02-05 Impact factor: 5.469

8. Hydroxyethylene isostere inhibitors of human immunodeficiency virus-1 protease: structure-activity analysis using enzyme kinetics, X-ray crystallography, and infected T-cell assays.

Authors: G B Dreyer; D M Lambert; T D Meek; T J Carr; T A Tomaszek; A V Fernandez; H Bartus; E Cacciavillani; A M Hassell; M Minnich
Journal: Biochemistry Date: 1992-07-28 Impact factor: 3.162

9. Three-dimensional structure of influenza A N9 neuraminidase and its complex with the inhibitor 2-deoxy 2,3-dehydro-N-acetyl neuraminic acid.

Authors: P Bossart-Whitaker; M Carson; Y S Babu; C D Smith; W G Laver; G M Air
Journal: J Mol Biol Date: 1993-08-20 Impact factor: 5.469

10. X-ray crystal structure of the complex of human leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor.

Authors: W Bode; A Z Wei; R Huber; E Meyer; J Travis; S Neumann
Journal: EMBO J Date: 1986-10 Impact factor: 11.598

7 in total

Comparison of protein surfaces using a genetic algorithm.

1. A new tool for the qualitative and quantitative analysis of protein surfaces using B-spline and density of surface neighborhood.

2. Crystallographic refinement of the three-dimensional structure of the FabD1.3-lysozyme complex at 2.5-A resolution.

3. Protein clefts in molecular recognition and function.

4. Molecular surface-volume and property matching to superpose flexible dissimilar molecules.

5. Molecular skins: a new concept for quantitative shape matching of a protein with its small molecule mimics.

6. Structure of myoglobin refined at 2-0 A resolution. II. Structure of deoxymyoglobin from sperm whale.

7. Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm.

8. Hydroxyethylene isostere inhibitors of human immunodeficiency virus-1 protease: structure-activity analysis using enzyme kinetics, X-ray crystallography, and infected T-cell assays.

9. Three-dimensional structure of influenza A N9 neuraminidase and its complex with the inhibitor 2-deoxy 2,3-dehydro-N-acetyl neuraminic acid.

10. X-ray crystal structure of the complex of human leukocyte elastase (PMN elastase) and the third domain of the turkey ovomucoid inhibitor.

1. A novel method of aligning molecules by local surface shape similarity.

2. Comparison of substructural epitopes in enzyme active sites using self-organizing maps.

3. FTIP: an accurate and efficient method for global protein surface comparison.

4. Mapping of ligand-binding cavities in proteins.

5. Protein surface representation and analysis by dimension reduction.

6. From the similarity analysis of protein cavities to the functional classification of protein families using cavbase.

7. VASP-E: specificity annotation with a volumetric analysis of electrostatic isopotentials.