Simulations and Experiments in Protein Folding
- Publication type:
- Chapter
- Metadata:
-
- Autoren
- Giovanni Settanni
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000344689900014&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1007/978-1-4939-1465-4_13
- ISBN-13
- 978-1-4939-1464-7
- Schlüsselwörter
- Kinetics
- Transition state
- Committor
- Phi-value
- Clustering
- Kinetic network
- Paginierung
- 289 - 306
- Buchtitel
- MOLECULAR MODELING OF PROTEINS: 2ND EDITION
- Datum der Veröffentlichung
- 2015
- Status
- Published
- Titel
- Simulations and Experiments in Protein Folding
- Ausgabe der Zeitschrift
- 1215
Data source: Web of Science (Lite)
- Other metadata sources:
-
- Autoren
- Giovanni Settanni
- DOI
- 10.1007/978-1-4939-1465-4_13
- ISBN-13
- 9781493914647
- Online publication date
- 2014
- Paginierung
- 289 - 306
- Buchtitel
- Methods in Molecular Biology
- Datum der Veröffentlichung
- 2015
- Status
- Published
- Herausgeber
- Springer New York
- Herausgeber URL
- http://dx.doi.org/10.1007/978-1-4939-1465-4_13
- Datum der Datenerfassung
- 2019
- Titel
- Simulations and Experiments in Protein Folding
Data source: Crossref
- Abstract
- The interplay between simulations and experiments of protein folding has largely contributed to the elucidation of many important aspects of the phenomenon. In this chapter, I briefly describe the experiments which provide information on the kinetics of the protein folding process, and help to characterize the folding transition state. Then, I show how to probe the kinetics of protein folding using molecular dynamics simulations, how to compare the simulations with the experiments and how to help and rationalize the latter, ultimately offering a molecular picture of the process. After the production of suitable molecular dynamics simulation data in the form of trajectories, the procedure involves sequentially the identification of the stable states of the protein, the identification of the transition pathways connecting the stable states, the identification of the transition state conformations, comparison with experimental results, and finally, the identification of the molecular determinants or reaction coordinates of the folding process, that is, the features that clearly help distinguishing the transition state from the stable states.
- Addresses
- Physics Department, Johannes Gutenberg Universität, Staudingerweg 9, 55128, Mainz, Germany, settanni@uni-mainz.de.
- Autoren
- Giovanni Settanni
- DOI
- 10.1007/978-1-4939-1465-4_13
- Open access
- false
- Schlüsselwörter
- Peptides
- Proteins
- Reproducibility of Results
- Protein Folding
- Algorithms
- Time Factors
- Molecular Dynamics Simulation
- Medium
- Paginierung
- 289 - 306
- Datum der Veröffentlichung
- 2015
- Status
- Published
- Datum der Datenerfassung
- 2014
- Titel
- Simulations and experiments in protein folding.
- Ausgabe der Zeitschrift
- 1215
Data source: Europe PubMed Central
- Abstract
- The interplay between simulations and experiments of protein folding has largely contributed to the elucidation of many important aspects of the phenomenon. In this chapter, I briefly describe the experiments which provide information on the kinetics of the protein folding process, and help to characterize the folding transition state. Then, I show how to probe the kinetics of protein folding using molecular dynamics simulations, how to compare the simulations with the experiments and how to help and rationalize the latter, ultimately offering a molecular picture of the process. After the production of suitable molecular dynamics simulation data in the form of trajectories, the procedure involves sequentially the identification of the stable states of the protein, the identification of the transition pathways connecting the stable states, the identification of the transition state conformations, comparison with experimental results, and finally, the identification of the molecular determinants or reaction coordinates of the folding process, that is, the features that clearly help distinguishing the transition state from the stable states.
- Autoren
- Giovanni Settanni
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/25330968
- DOI
- 10.1007/978-1-4939-1465-4_13
- Schlüsselwörter
- Algorithms
- Molecular Dynamics Simulation
- Peptides
- Protein Folding
- Proteins
- Reproducibility of Results
- Time Factors
- Paginierung
- 289 - 306
- Datum der Veröffentlichung
- 2015
- Status
- Published
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2015
- Titel
- Simulations and experiments in protein folding.
- Ausgabe der Zeitschrift
- 1215
Data source: PubMed
- Beziehungen:
- Property of