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Long proteins with unique optimal foldings in the H-P model

Oswin Aichholzer, David Bremner, Erik D. Demaine, Henk Meijer, Vera Sacristán, Michael Soss
2003 Computational geometry  
In this paper we consider a problem suggested by Brian Hayes in 1998: what proteins in the two-dimensional H-P model have unique optimal (minimum energy) foldings?  ...  The H-P (hydrophobic-hydrophilic) model is a simple combinatorial model designed to answer qualitative questions about the protein folding process.  ...  Acknowledgements The authors would like to thank Godfried Toussaint for pointing us to this topic and for organizing the workshop at which the research was initiated.  ... 
doi:10.1016/s0925-7721(02)00134-7 fatcat:3ny5736tizf3he66qo5xj3oge4

Long Proteins with Unique Optimal Foldings in the H-P Model [article]

Oswin Aichholzer, David Bremner, Erik D. Demaine, Henk Meijer, Vera Sacristán, Michael Soss
2002 arXiv   pre-print
In this paper we consider a problem suggested by Brian Hayes in 1998: what proteins in the two-dimensional H-P model have unique optimal (minimum energy) foldings?  ...  The H-P (hydrophobic-hydrophilic) model is a simple combinatorial model designed to answer qualitative questions about the protein folding process.  ...  Acknowledgements The authors would like to thank Godfried Toussaint for pointing us to this topic and for organizing the workshop at which the research was initiated.  ... 
arXiv:cs/0201018v1 fatcat:2bibnqy6wzbgbo6nd5rjhfiqbe

Hydrophobic forces and the length limit of foldable protein domains

M. M. Lin, A. H. Zewail
2012 Proceedings of the National Academy of Sciences of the United States of America  
We define N HP ðsÞ to be the degeneracy of self-avoiding compact folds with maximum H/P segregation, which is a function of s, the sequence of H and P residues along the chain.  ...  The final step is the further reduction of the fold space by choosing only those compact folds with hydrophobic residues (H) maximally segregated, in the sense of maximizing the number of H-H contacts,  ...  David Shaw for thoroughly going over the entire manuscript; we value his comments, which added to the clarity of the work presented.  ... 
doi:10.1073/pnas.1207382109 pmid:22665780 pmcid:PMC3382496 fatcat:7z5o6c6bbjaatbxbpxao5e7pfa

A replica exchange Monte Carlo algorithm for protein folding in the HP model

Chris Thachuk, Alena Shmygelska, Holger H Hoos
2007 BMC Bioinformatics  
In this work, we implement and evaluate the replica exchange Monte Carlo (REMC) method, which has already been applied very successfully to more complex protein models and other optimization problems with  ...  Furthermore, it scales well with sequence length, and it finds significantly better conformations on long biological sequences and sequences with a provably unique ground-state structure, which is believed  ...  Acknowledgements We would like to thank Neil Lesh, Michael Mitzenmacher and Sue Whitesides for providing us with their GTabu code, and Peter Grassberger for providing us with an implementation of PERM.  ... 
doi:10.1186/1471-2105-8-342 pmid:17875212 pmcid:PMC2071922 fatcat:ygnpdgzogjc2tjs42ptcaipoie

Forces of tertiary structural organization in globular proteins

K. Yue, K. A. Dill
1995 Proceedings of the National Academy of Sciences of the United States of America  
Proteins are modeled as copolymers of specific sequences of hydrophobic (H) and polar (P) monomers (HP model) configured as self-avoiding flights on simple three-dimensional cubic lattices.  ...  We report here a procedure that can find all the globally optimal conformations, the number of which defines the degeneracy of a sequence, for chains up to 88 monomers long.  ...  Third, to avoid burial of P monomers in the H-core, the H monomers at the center of the core must be contained in long H-segments of a sequence.  ... 
doi:10.1073/pnas.92.1.146 pmid:7816806 pmcid:PMC42834 fatcat:ffwmuiflurfbbasbh6lqxwax2y

Potential of genetic algorithms in protein folding and protein engineering simulations

Thomas Dandekar, Patrick Argos
1992 Protein Engineering Design & Selection  
Vast conformational spaces are efficiently searched as iIIustrated by the ab initio folding of a model protein of a four ß strand bundle.  ...  Cooperativity in the ß strand regions and a length of 3 -5 for the interconnecting loops was criticaI. Specific interaction sites were considerably less effective in driving the fold.  ...  In a model four ß strand structure the genetic a1gorithm reached smoothly a unique protein fold.  ... 
doi:10.1093/protein/5.7.637 pmid:1480618 fatcat:g4d33oocczhdpa4lbt7nmbvicq

Near-native Protein Structure Simulation

Stefka Fidanova
2007 Bioautomation  
Other is based on reduced models of proteins structure like hydrophobic-polar (HP) protein model. After that, the folding problem is defined like optimization problem.  ...  The protein folding problem is a fundamental problem in computational molecular biology and biochemical physics.  ...  Acknowledgements Stefka Fidanova was supported by the European Community grand RISCK 21 and by the Bulgarian Ministry of Education by the grand "Virtual screening and computer modeling for drug design  ... 
doaj:2aa6263617614478a935db0d219b7799 fatcat:hgokkj3bmjhj3l5ojuyi4egt24

Lattice protein design using Bayesian learning [article]

Tomoei Takahashi, George Chikenji, Kei Tokita
2021 arXiv   pre-print
However, the performance was not as good for the 3D lattice HP models compared to the 2D models. The performance of the 3D model improves on using a 20-letter lattice proteins.  ...  As a result, on applying the 2D lattice hydrophobic-polar (HP) model, our design method successfully finds an amino acid sequence for which the target conformation has a unique ground state.  ...  ACKNOWLEDGMENTS The authors are grateful to M. Ota, Nagoya University, for illuminating discussions. This work was supported by KAKENHI Nos. 19H03166 (G.C.) and 19K03650 (K.T.).  ... 
arXiv:2003.06601v5 fatcat:zlz7ykx4w5fvhoyszmxyt34q7y

Modeling study on the validity of a possibly simplified representation of proteins

Jun Wang, Wei Wang
2000 Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics  
The reduced sequences have a good foldability and fold to the same native structure of their optimized original ones.  ...  The folding characteristics of sequences reduced with a possibly simplified representation of five types of residues are shown to be similar to their original ones with the natural set of residues (20  ...  Indeed, this is true for the usual HP model (with E HH = −1 and E HP = E P P = 0) [4] and that used by Li, et al. (with E HH = −2.3, E HP = −1, and E P P = 0) [7] .  ... 
doi:10.1103/physreve.61.6981 pmid:11088391 fatcat:yuiutg6ao5gdhn57jhgqtm5bem

Page 4276 of Mathematical Reviews Vol. , Issue 2004e [page]

2004 Mathematical Reviews  
proteins with unique optimal foldings in the H-P model.  ...  In this paper we consider a prob- lem suggested by Brian Hayes in 1998: what proteins in the two- dimensional H-P model have unique optimal (minimum energy) foldings?  ... 

On the theory of folding kinetics for short proteins

Vijay S Pande, Alexander Yu Grosberg, Toyoichi Tanaka
1997 Folding & design  
First, proteins are the result of evolutionary 'sequence selection' to optimize the energy of the native state.  ...  Second, the overlap with the native state is a qualitatively suitable reaction coordinate for modeling folding kinetics. The former principle is bolder and better established.  ...  Acknowledgements We have benefited from discussions with JN Onuchic and EI Shakhnovich.  ... 
doi:10.1016/s1359-0278(97)00015-1 pmid:9135983 fatcat:mftasa73ynd7bdvp557fndjtdu

Properties of a Two Dimensional Model of RNA Folding [article]

Ben Y. Maron
2018 arXiv   pre-print
The properties of the H-P (hydrophobic-hydrophilic) model of protein folding has been well studied in the two dimensional orthogonal case, and we attempt to achieve similar results.  ...  We prove that (1) there is an infinite family of even-length sequences with unique optimal foldings, (2) there are two ideal foldings for an even length sequence and given a sequence is is quickly verifiable  ...  at Williams College for her guidance in editing and submitting this paper.  ... 
arXiv:1812.06284v1 fatcat:dqathmxqknaynchl6dza4tkjn4

A minimalist model protein with multiple folding funnels

C. R. Locker, R. Hernandez
2001 Proceedings of the National Academy of Sciences of the United States of America  
In this study, a minimalist model protein is designed to exhibit multiple long-lived states to explore the dynamics of the corresponding wild-type proteins.  ...  The results for the designed model protein prove by existence that the rugged energy landscape picture of protein folding can be generalized to include protein "misfolding" into long-lived states.  ...  The DS1 sequence, P H P N P N N N H P H P H P N N N H P H P H P N H H N, [2] is used in all of the reported simulations of this work and was chosen arbitrarily.  ... 
doi:10.1073/pnas.161438898 pmid:11470921 pmcid:PMC55375 fatcat:jzmcugkbyrakvlrdtcnfh5dnue

Exact methods for lattice protein models

Martin Mann, Rolf Backofen
2014 Bio-Algorithms and Med-Systems  
However, even in the simplest lattice protein models, the prediction of optimal structures is computationally difficult. Therefore, often, heuristic approaches are applied to find such conformations.  ...  By discretizing the structure space and simplifying the energy model over regular proteins, they enable detailed studies of protein structure formation and evolution.  ...  The existence of a unique native fold, i.e. lowest energy conformation, is a common criterion to name a model sequence protein-like.  ... 
doi:10.1515/bams-2014-0014 fatcat:z5ftb32mz5dupnry6a5oqwulxq

Funnel-like organization in sequence space determines the distributions of protein stability and folding rate preferred by evolution

Yu Xia, Michael Levitt
2004 Proteins: Structure, Function, and Bioinformatics  
The exhaustive nature of our study necessitates using simplified models of protein folding. We obtain a stability map and a folding rate map in sequence space.  ...  Comparison of the two maps reveals a common organizational principle: optimality decreases more or less uniformly with distance from the optimal sequence in the sequence space.  ...  Each lattice vertex represents a protein residue and is labeled by H (hydrophobic) or P (polar). 27 We use a pairwise contact energy function with e HH ϭ Ϫ1 ϩ ␣, e HP ϭ e PP ϭ ␣.  ... 
doi:10.1002/prot.10563 pmid:14997545 pmcid:PMC2745081 fatcat:wsw77dm5n5epzh2hidybk2sgdq
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