A linear-time algorithm for solving the molecular distance geometry problem with exact inter-atomic distances
نویسندگان
چکیده
We describe a linear-time algorithm for solving the molecular distance geometry problem with exact distances between all pairs of atoms. This problem needs to be solved in every iteration of general distance geometry algorithms for protein modeling such as the EMBED algorithm by Crippen and Havel (Distance Geometry and Molecular Conformation, Wiley, 1988). However, previous approaches to the problem rely on decomposing an distance matrix or minimizing an error function and require O(n2) to O(n3) floating point operations. The linear-time algorithm will provide a much more efficient approach to the problem, especially in large-scale applications. It exploits the problem structure and hence is able to identify infeasible data more easily as well.
منابع مشابه
Solving the competitive facility location problem considering the reactions of competitor with a hybrid algorithm including Tabu Search and exact method
In this paper, a leader–follower competitive facility location problem considering the reactions of the competitors is studied. A model for locating new facilities and determining levels of quality for the facilities of the leader firm is proposed. Moreover, changes in the location and quality of existing facilities in a competitive market where a competitor offers the same goods or services ar...
متن کاملA Geometric Build-Up Algorithm for Solving the Molecular Distance Geometry Problem with Sparse Distance Data
Nuclear magnetic resonance (NMR) structure modeling usually produces a sparse set of inter-atomic distances in protein. In order to calculate the three-dimensional structure of protein, current approaches need to estimate all other “missing” distances to build a full set of distances. However, the estimation step is costly and prone to introducing errors. In this report, we describe a geometric...
متن کاملA Branch-and-Prune Algorithm for the Molecular Distance Geometry Problem
The Molecular Distance Geometry Problem consists in finding the positions in R of the atoms of a molecule, given some of the inter-atomic distances. We show that under an additional requirement on the given distances (which is realistic from the chemical point of view) this can be transformed to a combinatorial problem. We propose a Branch-and-Prune algorithm for the solution of this problem an...
متن کاملGrover’s Algorithm applied to the Molecular Distance Geometry Problem
Grover’s algorithm is a quantum algorithm for searching in unstructured databases. Due to the properties of quantum mechanics, it provides a quadratic speedup over its classical counterparts. We present a new application of the algorithm to the Molecular Distance Geometry Problem. This problem is related to the determination of the tridimensional structure of a molecule based on the knowledge o...
متن کاملA note on "A branch-and-prune algorithm for the molecular distance geometry problem"
The Molecular Distance Geometry Problem consists in finding the positions in R of the atoms of a molecule, given some of the inter-atomic distances. We show that under an additional requirement on the given distances (which is realistic from the chemical point of view) this can be transformed to a combinatorial problem. We propose a Branch-and-Prune algorithm for the solution of this problem an...
متن کاملذخیره 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 ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- J. Global Optimization
دوره 22 شماره
صفحات -
تاریخ انتشار 2002