Results 1 
5 of
5
Rapid protein sidechain packing via tree decomposition
 Research in Computational Molecular Biology, Lecture Notes in Computer Science
, 2005
"... Abstract. This paper proposes a novel tree decomposition based sidechain assignment algorithm, which can obtain the globally optimal solution of the sidechain packing problem very efficiently. Theoretically, the computational complexity of this algorithm is O((N +M)n tw+1 rot) where N is the numbe ..."
Abstract

Cited by 26 (1 self)
 Add to MetaCart
(Show Context)
Abstract. This paper proposes a novel tree decomposition based sidechain assignment algorithm, which can obtain the globally optimal solution of the sidechain packing problem very efficiently. Theoretically, the computational complexity of this algorithm is O((N +M)n tw+1 rot) where N is the number of residues in the protein, M the number of interacting residue pairs, nrot the average number of rotamers for each residue and tw( = O(N 2 3 log N)) the tree width of the residue interaction graph. Based on this algorithm, we have developed a sidechain prediction program SCATD (Side Chain Assignment via Tree Decomposition). Experimental results show that after the Goldstein DEE is conducted, nrot is around 3.5, tw is only 3 or 4 for most of the test proteins in the SCWRL benchmark and less than 10 for all the test proteins. SCATD runs up to 90 times faster than SCWRL 3.0 on some large proteins in the SCWRL benchmark and achieves an average of five times faster speed on all the test proteins. If only the postDEE stage is taken into consideration, then our treedecomposition based energy minimization algorithm is more than 200 times faster than that in SCWRL 3.0 on some large proteins. SCATD is freely available for academic research upon request. 1
Fast and accurate algorithms for protein sidechain packing
, 2006
"... This article studies the protein sidechain packing problem using the treedecomposition of a protein structure. To obtain fast and accurate protein sidechain packing, protein structures are modeled using a geometric neighborhood graph, which can be easily decomposed into smaller blocks. Therefor ..."
Abstract

Cited by 11 (1 self)
 Add to MetaCart
(Show Context)
This article studies the protein sidechain packing problem using the treedecomposition of a protein structure. To obtain fast and accurate protein sidechain packing, protein structures are modeled using a geometric neighborhood graph, which can be easily decomposed into smaller blocks. Therefore, the sidechain assignment of the whole protein can be assembled from the assignment of the small blocks. Although we will show that the sidechain packing problem is still NPhard, we can achieve a treedecompositionbased globally optimal algorithm with time complexity of O(Nn tw+1 rot) and several polynomialtime approximation schemes (PTAS), where N is the number of residues contained in the protein, nrot the average number of rotamers for each residue, and tw = O(N 2/3 log N) the treewidth of the protein structure graph. Experimental results indicate that after Goldstein deadend elimination is conducted, nrot is very small and tw is equal to 3 or 4 most of the time. Based on the globally optimal algorithm, we developed a protein sidechain assignment program TreePack, which runs up to 90 times faster than SCWRL 3.0, a widelyused sidechain packing program, on some large test proteins in the SCWRL benchmark database and an average of five times faster on all the test proteins in this database. There are also some realworld
Large scale protein sidechain packing based on maximum edgeweight clique ¯nding algorithm
 Proc. 2005 International Joint Conference of InCoB, AASBi, and KSBI(BIOINFO2005
"... The protein sidechain packing problem is computationally known to be NPcomplete [1]. A number of approaches has been proposed for sidechain packing. As the size of the protein becomes larger, the sampling space increases exponentially. Hence, large scale protein sidechain packing In this regard, ..."
Abstract

Cited by 1 (1 self)
 Add to MetaCart
(Show Context)
The protein sidechain packing problem is computationally known to be NPcomplete [1]. A number of approaches has been proposed for sidechain packing. As the size of the protein becomes larger, the sampling space increases exponentially. Hence, large scale protein sidechain packing In this regard, we had also presented a maximum edgeweight clique based algorithm for protein
proteins STRUCTURE O FUNCTION O BIOINFORMATICS From coarsegrain to allatom: Toward multiscale analysis of protein landscapes
"... Multiscale techniques have recently emerged as promising tools to combine the efficiency of coarsegrain simulations with the detail of allatom simulations for the characterization of a broad range of molecular systems in fields such as material science and biophysics. Recent work has focused on ..."
Abstract
 Add to MetaCart
Multiscale techniques have recently emerged as promising tools to combine the efficiency of coarsegrain simulations with the detail of allatom simulations for the characterization of a broad range of molecular systems in fields such as material science and biophysics. Recent work has focused on the definition of strategies that combine