Hydrophobic-polar protein folding model: Difference between revisions
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The HP model can be expressed in both two and three dimensions, generally with [[square lattice]]s, although triangular lattices have been used as well. It has also been studied on general regular lattices.<ref>{{cite journal |author= Bechini, A. |title= On the characterization and software implementation of general protein lattice models |journal= PLoS ONE| volume= 8 |issue= 3 |year=2013|pages= e59504 |doi= 10.1371/journal.pone.0059504}}</ref> |
The HP model can be expressed in both two and three dimensions, generally with [[square lattice]]s, although triangular lattices have been used as well. It has also been studied on general regular lattices.<ref>{{cite journal |author= Bechini, A. |title= On the characterization and software implementation of general protein lattice models |journal= PLoS ONE| volume= 8 |issue= 3 |year=2013|pages= e59504 |doi= 10.1371/journal.pone.0059504}}</ref> |
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Randomized search algorithms are often used to tackle the HP folding problem. This includes [[stochastic]], [[evolutionary algorithm]]s like the [[Monte Carlo method]], [[genetic algorithms]], and [[ant colony optimization]]. While no method has been able to calculate the experimentally determined minimum energetic state for long protein sequences, the most advanced methods today are able to come close.<ref name="bui2005">{{cite journal |author=Bui T.N., Sundarraj G. |title=An efficient genetic algorithm for predicting protein tertiary structures in the 2D HP model |journal=Gecco'05 |year=2005 |doi=10.1145/1068009.1068072 |pages=385 }}</ref><ref name="shmygelska2003">{{cite journal |author=Shmygelska A., Hoos H.H. |title=An improved ant colony optimisation algorithm for the 2D HP protein folding problem |journal=Proc. of the 16th Canadian Conference on Artificial Intelligence (AI'2003)|volume=2671 |pages=400–417 |year=2003}}</ref> |
Randomized search algorithms are often used to tackle the HP folding problem. This includes [[stochastic]], [[evolutionary algorithm]]s like the [[Monte Carlo method]], [[genetic algorithms]], and [[ant colony optimization]]. While no method has been able to calculate the experimentally determined minimum energetic state for long protein sequences, the most advanced methods today are able to come close.<ref name="bui2005">{{cite journal |author=Bui T.N., Sundarraj G. |title=An efficient genetic algorithm for predicting protein tertiary structures in the 2D HP model |journal=Gecco'05 |year=2005 |doi=10.1145/1068009.1068072 |pages=385 }}</ref><ref name="shmygelska2003">{{cite journal |author=Shmygelska A., Hoos H.H. |title=An improved ant colony optimisation algorithm for the 2D HP protein folding problem |journal=Proc. of the 16th Canadian Conference on Artificial Intelligence (AI'2003)|volume=2671 |pages=400–417 |year=2003 |doi=10.1007/3-540-44886-1_30}}</ref> |
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Even though the HP model abstracts away many of the details of protein folding, it is still an [[NP-hard]] problem on both 2D and 3D lattices.<ref name="crescenzi1998">{{cite journal |author=Crescenzi P., Goldman D., Papadimitriou C., Piccolboni A., Yannakakis M. |title=On the complexity of protein folding |journal=Macromolecules |volume=5 |issue=1 |pages=27–40 |year=1998 |pmid=9773342}}</ref> |
Even though the HP model abstracts away many of the details of protein folding, it is still an [[NP-hard]] problem on both 2D and 3D lattices.<ref name="crescenzi1998">{{cite journal |author=Crescenzi P., Goldman D., Papadimitriou C., Piccolboni A., Yannakakis M. |title=On the complexity of protein folding |journal=Macromolecules |volume=5 |issue=1 |pages=27–40 |year=1998 |pmid=9773342 |doi=10.1145/279069.279089}}</ref> |
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Recently, a Monte Carlo method, named FRESS, was developed and appears to perform well on HP models.<ref name="zhang2007">{{cite journal |author=Jinfeng Zhang, S. C. Kou, Jun S. Liu | title=Polymer structure optimization and simulation via a fragment re-growth Monte Carlo |journal=J. Chem. Phys. |volume=126 |pages=225101 |year=2007 |doi=10.1063/1.2736681 |pmid=17581081 |issue=22}}</ref> |
Recently, a Monte Carlo method, named FRESS, was developed and appears to perform well on HP models.<ref name="zhang2007">{{cite journal |author=Jinfeng Zhang, S. C. Kou, Jun S. Liu | title=Polymer structure optimization and simulation via a fragment re-growth Monte Carlo |journal=J. Chem. Phys. |volume=126 |pages=225101 |year=2007 |doi=10.1063/1.2736681 |pmid=17581081 |issue=22}}</ref> |
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Revision as of 18:41, 24 May 2014
The hydrophobic-polar protein folding model is a highly simplified model for examining protein folds in space. First proposed by Dill in 1985, it is the most known type of lattice protein: it stems from the observation that hydrophobic interactions between amino acid residues are the driving force for proteins folding into their native state.[1] All amino acid types are classified as either hydrophobic (H) or polar (P), and the folding of a protein sequence is defined as a self-avoiding walk in a 2D or 3D lattice. The HP model imitates the hydrophobic effect by assigning a negative (favorable) weight to interactions between adjacent, non-covalently bound H residues. Proteins that have minimum energy are assumed to be in their native state.
The HP model can be expressed in both two and three dimensions, generally with square lattices, although triangular lattices have been used as well. It has also been studied on general regular lattices.[2]
Randomized search algorithms are often used to tackle the HP folding problem. This includes stochastic, evolutionary algorithms like the Monte Carlo method, genetic algorithms, and ant colony optimization. While no method has been able to calculate the experimentally determined minimum energetic state for long protein sequences, the most advanced methods today are able to come close.[3][4]
Even though the HP model abstracts away many of the details of protein folding, it is still an NP-hard problem on both 2D and 3D lattices.[5]
Recently, a Monte Carlo method, named FRESS, was developed and appears to perform well on HP models.[6]
See also
References
- ^ Dill K.A. (1985). "Theory for the folding and stability of globular proteins". Biochemistry. 24 (6): 1501–9. doi:10.1021/bi00327a032. PMID 3986190.
- ^ Bechini, A. (2013). "On the characterization and software implementation of general protein lattice models". PLoS ONE. 8 (3): e59504. doi:10.1371/journal.pone.0059504.
{{cite journal}}: CS1 maint: unflagged free DOI (link) - ^ Bui T.N., Sundarraj G. (2005). "An efficient genetic algorithm for predicting protein tertiary structures in the 2D HP model". Gecco'05: 385. doi:10.1145/1068009.1068072.
- ^ Shmygelska A., Hoos H.H. (2003). "An improved ant colony optimisation algorithm for the 2D HP protein folding problem". Proc. of the 16th Canadian Conference on Artificial Intelligence (AI'2003). 2671: 400–417. doi:10.1007/3-540-44886-1_30.
- ^ Crescenzi P., Goldman D., Papadimitriou C., Piccolboni A., Yannakakis M. (1998). "On the complexity of protein folding". Macromolecules. 5 (1): 27–40. doi:10.1145/279069.279089. PMID 9773342.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Jinfeng Zhang, S. C. Kou, Jun S. Liu (2007). "Polymer structure optimization and simulation via a fragment re-growth Monte Carlo". J. Chem. Phys. 126 (22): 225101. doi:10.1063/1.2736681. PMID 17581081.
{{cite journal}}: CS1 maint: multiple names: authors list (link)