Extending the geometric build-up algorithm for the molecular distance geometry problem

Authors:
Ricardo dos Santos Carvalho;Carlile Lavor;Fábio Protti
Affiliations:
Universidade Federal do Rio de Janeiro (IM/NCE-UFRJ), Caixa Postal 2324, CEP 20001-970, Rio de Janeiro, RJ, Brazil;Universidade Estadual de Campinas (IMECC-UNICAMP), Caixa Postal 6065, CEP 13081-970, Campinas, SP, Brazil;Universidade Federal do Rio de Janeiro (IM/NCE-UFRJ), Caixa Postal 2324, CEP 20001-970, Rio de Janeiro, RJ, Brazil
Venue:
Information Processing Letters
Year:
2008

Citing 8
Cited 3

Molecular Modeling of Proteins and Mathematical Prediction of Protein Structure

SIAM Review
Global Continuation for Distance Geometry Problems

SIAM Journal on Optimization
Distance Geometry Optimization for Protein Structures

Journal of Global Optimization
A linear-time algorithm for solving the molecular distance geometry problem with exact inter-atomic distances

Journal of Global Optimization
A Geometric Build-Up Algorithm for Solving the Molecular Distance Geometry Problem with Sparse Distance Data

Journal of Global Optimization
Large-Scale Molecular Optimization from Distance Matrices by a D. C. Optimization Approach

SIAM Journal on Optimization
Solving Large Scale Molecular Distance Geometry Problems by a Smoothing Technique via the Gaussian Transform and D.C. Programming

Journal of Global Optimization
An updated geometric build-up algorithm for solving the molecular distance geometry problems with sparse distance data

Journal of Global Optimization

On the computation of protein backbones by using artificial backbones of hydrogens

Journal of Global Optimization
The discretizable molecular distance geometry problem

Computational Optimization and Applications
A discrete search algorithm for finding the structure of protein backbones and side chains

International Journal of Bioinformatics Research and Applications

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Abstract

One of the most important problems in computational biology is the determination of the three-dimensional structure of a protein using the amino acid sequence that generates it. This task can be experimentally performed by using NMR techniques. However, NMR data usually provide only a sparse set of distances between atoms of a molecule. In this case, the aim is to determine its three-dimensional structure using a set of distances for only some pairs of atoms. This problem is known as the Molecular Distance Geometry Problem (MDGP). This work extends the Geometric Build-up Algorithm (GBA) by Dong and Wu, proposed to solve instances of the MDGP. Computational results show that the presented approach, the Extended Geometric Build-up Algorithm (EGBA), is capable of dealing with instances not previously solved by the GBA.