Paper Info
Title
FROST: Revisited and Distributed
Abstract
FROST (Fold Recognition-Oriented Search Tool) is a software whose purpose is to assign a 3D structure to a protein sequence. It is based on a series of filters and uses a database of about 1200 known 3D structures, each one associated with empirically determined score distributions. FROST uses these distributions to normalize the score obtained when a protein sequence is aligned with a particular 3D structure. Computing these distributions is extremely time consuming; it requires solving about 1,200,000 hard combinatorial optimization problems and takes about 40 days on a 2.4 GHz computer. This paper describes how FROST has been successfully redesigned and structured in modules and independent tasks. The new package organization allows these tasks to be distributed and executed in parallel using a centralized dynamic load balancing strategy. On a cluster of 12 PCs, computing the score distributions takes now about 3 days which represents a parallelization efficiency of about 1.
Year
DOI
Venue
2005
10.1109/IPDPS.2005.231
IPDPS
Keywords
Field
DocType
hard combinatorial optimization problem,fold recognition-oriented search tool,score distribution,independent task,ghz computer,parallelization efficiency,protein sequence,centralized dynamic load,time consuming,new package organization,distributed computing,fold recognition,databases,multi threading,parallel algorithm,parallel algorithms,amino acids,packaging,resource allocation,computational biology,proteins,protein threading
Multithreading,Normalization (statistics),Combinatorial optimization problem,Frost,Parallel algorithm,Computer science,Threading (protein sequence),Parallel computing,Algorithm,Software,Resource allocation,Distributed computing
Conference
ISBN
Citations 
PageRank 
0-7695-2312-9
2
0.42
References 
Authors
9
4
Name
Order
Citations
PageRank
Vincent Poirriez1897.64
Rumen Andonov226924.24
Antoine Marin320.42
Jean-Francois Gibrat4101.30