Few Optimal Foldings of HP Protein Chains on Various Lattices ∗

نویسندگان

  • Sheung-Hung Poon
  • Shripad Thite
چکیده

We consider whether or not protein chains in the HP model have unique or few optimal foldings. We solve the conjecture proposed by Aichholzer et al. that the open chain L2k−1 = (HP )(PH) for k ≥ 3 has exactly two optimal foldings on the square lattice. We show that some closed and open chains have unique optimal foldings on the hexagonal and triangular lattices, respectively.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure Prediction Better than 86% of Optimal

This paper considers the protein energy minimization problem for lattice and off-lattice protein folding models that explicitly represent side chains. Lattice models of proteins have proven useful tools for reasoning about protein folding in unrestricted continuous space through analogy. This paper provides the first illustration of how rigorous algorithmic analyses of lattice models can lead t...

متن کامل

Local Interactions and Protein Folding: A Model Study on the Square and Triangular Lattices

We study a simple heteropolymer model containing sequence-independent local interactions on both square and triangular lattices. Sticking to a two-letter code, we investigate the model for varying strength κ of the local interactions; κ = 0 corresponds to the well-known HP model [K.F. Lau and K.A. Dill, Macromolecules 22, 3986 (1989)]. By exhaustive enumerations for short chains, we obtain all ...

متن کامل

An integer programming model for protein structure prediction using the 3D-HP side chain model

In spite of the fact thatmany simplifiedmodel variants of protein structure prediction have beenwidely studied in the past years, few attention has been given to discretemodels with side chains, for which there is no specific benchmark. In this paper, we propose an integer programming model for the 3D-HP side chain protein structure prediction problem. The model accounts for the energy resultin...

متن کامل

Local Interactions and Protein Folding : A ModelStudy

We study a simple heteropolymer model containing sequence-independent local interactions on both square and triangular lattices. Sticking to a two-letter code, we investigate the model for varying strength of the local interactions; = 0 corresponds to the well-known HP model K.F. Lau and K.A. Dill, Macromolecules 22, 3986 (1989)]. By exhaustive enumerations for short chains, we obtain all struc...

متن کامل

ar X iv : c s . C G / 0 20 10 18 v 1 2 1 Ja n 20 02 Long Proteins with Unique Optimal Foldings in the H - P Model ⋆

It is widely accepted that (1) the natural or folded state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state determined by their amino acid sequence. The H-P (hydrophobic-hydrophilic) model is a simple combinatorial model designed to answer qualitative questions about the protein folding process. In this paper we consider a problem suggested by Brian ...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 2006