A 2O(n1-(1/d)log n) Time Algorithm for d-Dimensional Protein Folding in the HP-Model

نویسندگان

  • Bin Fu
  • Wei Wang
چکیده

The protein folding problem in the HP-model is NP-hard in both 2D and 3D [4, 6]. The problem is to put a sequence, consisting of two characters H and P, on a d-dimensional grid to have the maximal number of HH contacts. We design a 2 1− 1 d log n) time algorithm for ddimensional protein folding in the HP-model. In particular, our algorithm has O(2 √ n log ) and O(2 2 3 log ) computational time in 2D and 3D respectively. The algorithm is derived via our separator theorem for points on a d-dimensional grid. For example, for a set of n points P on a 2-dimensional grid, there is a separator with at most 1.129 √ n points that partitions P into two sides with at most ( 2 3 )n points on each side. Our separator theorem for grid points has a greatly reduced upper bound than that for the general planar graph [2].

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

Geometric Separators and Their Applications to Protein Folding in the HP-Model

We develop a new method for deriving a geometric separator for a set of grid points. Our separator has a linear structure, which can effectively partition a grid graph. For example, we prove that for a grid graph G with a set of n points P in a two-dimensional grid, there is a separator with at most 1.129 √ n points in P that partitions G into two disconnected grid graphs each with at most 2n 3...

متن کامل

Run-time Estimates for Protein Folding Simulation in the H-P Model

The hydrophobic-hydrophilic (H-P) model for protein folding was introduced by Dill et al. [6]. A problem instance consists of a sequence of amino acids, each labeled as either hydrophobic (H) or hydrophilic (P). The sequence must be placed on a 2D or 3D grid without overlapping, so that adjacent amino acids in the sequence remain adjacent in the grid. The goal is to minimize the energy, which i...

متن کامل

On the Difference Between Closest, Furthest, and Orthogonal Pairs: Nearly-Linear vs Barely-Subquadratic Complexity in Computational Geometry

Point location problems for n points in d-dimensional Euclidean space (and lp spaces more generally) have typically had two kinds of running-time solutions: (Nearly-Linear) less than d ·n log n time, or (Barely-Subquadratic) f (d) ·n2−1/Θ(d) time, for various functions f . For small d and large n, “nearly-linear” running times are generally feasible, while the “barelysubquadratic” times are gen...

متن کامل

Fine-Grained Complexity of Coloring Unit Disks and Balls

On planar graphs, many classic algorithmic problems enjoy a certain “square root phenomenon” and can be solved significantly faster than what is known to be possible on general graphs: for example, Independent Set, 3-Coloring, Hamiltonian Cycle, Dominating Set can be solved in time 2O( √ n) on an n-vertex planar graph, while no 2o(n) algorithms exist for general graphs, assuming the Exponential...

متن کامل

Efficient Approximation Algorithms for Point-set Diameter in Higher Dimensions

We study the problem of computing the diameter of a  set of $n$ points in $d$-dimensional Euclidean space for a fixed dimension $d$, and propose a new $(1+varepsilon)$-approximation algorithm with $O(n+ 1/varepsilon^{d-1})$ time and $O(n)$ space, where $0 < varepsilonleqslant 1$. We also show that the proposed algorithm can be modified to a $(1+O(varepsilon))$-approximation algorithm with $O(n+...

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 2004