The inverse protein folding problem on 2D and 3D lattices

In this paper we investigate the inverse protein folding (IPF) problem under the Canonical model on 3D and 2D lattices [W.E. Hart, On the computational complexity of sequence design problems, Proceedings of the First Annual International Conference on Computational Molecular Biology 1997, pp. 128-136; E.I. Shakhnovich, A.M. Gutin, Engineering of stable and fast-folding sequences of model proteins, Proc. Natl. Acad. Sci. 90 (1993) 7195-7199]. In this problem, we are given a contact graph G=(V,E) of a protein sequence that is embeddable in a 3D (respectively, 2D) lattice and an integer 1=

[1]  Volker Heun,et al.  Approximate protein folding in the HP side chain model on extended cubic lattices , 1999, Discret. Appl. Math..

[2]  David S. Johnson,et al.  Computers and Intractability: A Guide to the Theory of NP-Completeness , 1978 .

[3]  K. Dill,et al.  A lattice statistical mechanics model of the conformational and sequence spaces of proteins , 1989 .

[4]  Richard H. Lathrop,et al.  The threading approach to the inverse protein folding problem , 1997, RECOMB '97.

[5]  Refael Hassin,et al.  Complexity of finding dense subgraphs , 2002, Discret. Appl. Math..

[6]  Drexler Ke,et al.  Molecular engineering: An approach to the development of general capabilities for molecular manipulation. , 1981 .

[7]  Mihalis Yannakakis,et al.  On the Complexity of Protein Folding , 1998, J. Comput. Biol..

[8]  Flavio Seno,et al.  Structure‐based design of model proteins , 1998, Proteins.

[9]  E. Shakhnovich,et al.  Engineering of stable and fast-folding sequences of model proteins. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[10]  Hisao Tamaki,et al.  Greedily Finding a Dense Subgraph , 2000, J. Algorithms.

[11]  Scott Wilson.  The Protein Folding Problem and Tertiary Structure Prediction , 1994, Birkhäuser Boston.

[12]  Frank Thomson Leighton,et al.  Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete , 1998, RECOMB '98.

[13]  William E. Hart,et al.  Invariant Patterns in Crystal Lattices: Implications for Protein Folding Algorithms (Extended Abstract) , 1996, CPM.

[14]  K E Drexler,et al.  Molecular engineering: An approach to the development of general capabilities for molecular manipulation. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[15]  William E. Hart,et al.  Fast protein folding in the hydrophobic-hydrophilic model within three-eights of optimal , 1995, STOC '95.

[16]  Wolfgang Maass,et al.  Approximation schemes for covering and packing problems in image processing and VLSI , 1985, JACM.

[17]  William E. Hart,et al.  On the Intractability of Protein Folding with a Finite Alphabet of Amino Acids , 1999, Algorithmica.

[18]  Piotr Berman,et al.  Approximation algorithms for MAX-MIN tiling , 2003, J. Algorithms.

[19]  Dorit S. Hochba,et al.  Approximation Algorithms for NP-Hard Problems , 1997, SIGA.

[20]  Deutsch,et al.  New algorithm for protein design. , 1995, Physical review letters.

[21]  Jon M. Kleinberg,et al.  Efficient algorithms for protein sequence design and the analysis of certain evolutionary fitness landscapes , 1999, J. Comput. Biol..

[22]  William E. Hart,et al.  Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure Prediction Better than 86% of Optimal , 1997, J. Comput. Biol..

[23]  K. Dill,et al.  Inverse protein folding problem: designing polymer sequences. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[24]  U. Feige,et al.  On the densest k-subgraph problems , 1997 .

[25]  J. Ponder,et al.  Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes. , 1987, Journal of molecular biology.

[26]  K. Dill,et al.  Designing amino acid sequences to fold with good hydrophobic cores. , 1995, Protein engineering.

[27]  D. Yee,et al.  Principles of protein folding — A perspective from simple exact models , 1995, Protein science : a publication of the Protein Society.

[28]  William E. Hart.  On the computational complexity of sequence design problems , 1997, RECOMB '97.

[29]  Giancarlo Mauri,et al.  Approximation algorithms for protein folding prediction , 1999, SODA '99.