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 |
MARC
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| 245 | 0 | 0 | |a Protein folding in silico : |b protein folding versus protein structure prediction / |c edited by Irena Roterman-Konieczna. |
| 260 | |a Philadelphia, Pa : |b Woodhead Pub., |c 2012. | ||
| 300 | |a 1 online resource (xxxii, 208 pages) : |b illustrations (some color). | ||
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| 490 | 1 | |a Woodhead Publishing series in biomedicine ; |v no. 22 | |
| 504 | |a Includes bibliographical references and index. | ||
| 520 | |a 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 model that attempts to simulate as far as possible the folding process as it takes place in vivo, and attempts to construct a mechanistic model on the basis of the predictions made. The opening chapters discuss the early stage intermediate and late stage intermediate models, followed by a discussion of structural information that affects the interpretation of the folding process. The second half of the book covers a variety of topics including ligand binding site recognition, the "fuzzy oil drop" model and its use in simulation of the polypeptide chain, and misfolded proteins. The book ends with an overview of a number of other ab initio methods for protein structure predictions and some concluding remarks. Discusses a range of ab initio models for protein structure predictionIntroduces a unique model based on experimental observationsDescribes various methods for the quantitative assessment of the presented models from the viewpoint of information theory. | ||
| 505 | 0 | |a 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. | |
| 505 | 8 | |a 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. | |
| 505 | 8 | |a 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. | |
| 505 | 8 | |a 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. | |
| 505 | 8 | |a 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. | |
| 500 | |a ScienceDirect eBook - Biomedical Science and Medicine 2012 (Elsevier and Woodhead) |5 TMurS | ||
| 650 | 0 | |a Proteins |x Structure |x Computer simulation. | |
| 650 | 0 | |a Protein folding. | |
| 650 | 0 | |a Mathematical models. | |
| 700 | 1 | |a Roterman-Konieczna, Irena, |e editor. | |
| 730 | 0 | |a WORLDSHARE SUB RECORDS | |
| 758 | |i has work: |a Protein folding in silico (Text) |1 https://id.oclc.org/worldcat/entity/E39PCGTFfc3DkQrpDqwyxCJqwC |4 https://id.oclc.org/worldcat/ontology/hasWork | ||
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| 830 | 0 | |a Woodhead Publishing series in biomedicine ; |v no. 22. | |
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