Protein folding in silico : protein folding versus protein structure prediction /
Protein folding is a process by which a protein structure assumes its functional shape of conformation, and has been the subject of research since the publication of the first software tool for protein structure prediction. Protein folding in silico approaches this issue by introducing an ab initio...
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| Other Authors: | |
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| Format: | Electronic eBook |
| Language: | English |
| Published: |
Philadelphia, Pa :
Woodhead Pub.,
2012.
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| Series: | Woodhead Publishing series in biomedicine ;
no. 22. |
| Subjects: | |
| Online Access: | CONNECT |
Table of Contents:
- Cover; Protein folding in silico: Protein folding versus protein structure prediction; Copyright; Dedication; Contents; List of figures; List of tables; About the editor; List of contributors; Introduction; Reference; 1The early-stage intermediate; 1.1 Geometric model; 1.2 Structural alphabet; 1.3 Contingency table; 1.4 In search of structural similarities; 1.5 References; 1.6 Suggested reading; 2The late-stage intermediate; 2.1 The "fuzzy oil drop" model; 2.2 Quantitative description of the hydrophobic core; 2.3 Protein characteristics with respect to the hydrophobic core.
- 2.4 Simulation of late-stage folding2.5 References; 2.6 Suggested reading; 3Structural information involved in the interpretation of the stepwise protein folding process; 3.1 Balancing the quantity of information in the amino acid sequence and the early-stage intermediate; 3.2 Zones on the Ramachandran map; 3.3 References; 3.4 Suggested reading; 4 The divergence entropy characterizing the internal force field in proteins; 4.1 Internal force field for nonbonding interactions; 4.2 The impact of ligands; 4.3 Structures of homodimers
- protein-protein interaction.
- 4.4 Protein containing a catalytic center4.5 The role of exons; 4.6 Conclusions; 4.7 References; 5Ligand-binding-site recognition; 5.1 General model; 5.2 ROC curves; 5.3 Summary; 5.4 References; 5.5 Suggested reading; 6Use of the "fuzzy oil drop" model to identify the complexation area in protein homodimers; 6.1 General description; 6.2 ROC curves; 6.3 Conclusions; 6.4 References; 6.5 Suggested reading; 7Simulation of the polypeptide chain folding process using the "fuzzy oil drop" model; 7.1 Simulation of the folding process in the presence of an external hydrophobic force field.
- 7.2 Folding in the presence of a ligand7.3 Influence of external factors on polypeptide chain folding; 7.4 References; 7.5 Suggested reading; 8Misfolded proteins; 8.1 Introduction; 8.2In silico experiment; 8.3 Conclusions; 8.4 Appendix 1: details of the molecular dynamics simulation; 8.5 Appendix 2: details of the cluster analysis; 8.6 References; 8.7 Suggested reading; 9 A short description of otherselected ab initio methods forprotein structure prediction; 9.1 Introduction; 9.2 Simplifying the geometric model and the field function; 9.3 Lattice model; 9.4 ROSETTA.
- 9.5 In search of a global minimum
- force field deformation9.6 References; 9.7 Suggested reading; 9.8 Selected servers oriented toward protein structure prediction available on the Internet; Conclusion; 10.1 Acknowledgements; 10.2 References; 10.3 Suggested reading; Index.
