Revised paper, 5/28/2010

revision26may2010.tar
revisedResponseToReviewers: Final response to referees
new.pdf: revision
diff.pdf: differences, obtained using Latexdiff

Supplementary Data

The following sequences were used in benchmarking tests for the paper, "On Lattice Protein Structure Prediction Revisited", submitted by Ivan Dotu, Manuel Cebrian, Pascal Van Hentenryck, Peter Clote to IEEE Transactions on Computational Biology and Bioinformatics.

HP-sequences used in benchmarking tests

Harvard Instances

HPHHPPHHHHPHHHPPHHPPHPHHHPHPHHPPHHPPPHPPPPPPPPHH
HHHHPHHPHHHHHPPHPPHHPPHPPPPPPHPPHPPPHPPHHPPHHHPH
PHPHHPHHHHHHPPHPHPPHPHHPHPHPPPHPPHHPPHHPPHPHPPHP
PHPHHPPHPHHHPPHHPHHPPPHHHHHPPHPHHPHPHPPPPHPPHPHP
PPHPPPHPHHHHPPHHHHPHHPHHHPPHPHPHPPHPPPPPPHHPHHPH
HHHPPPHHPHPHHPHHPHHPHPPPPPPPHPHPPHPPPHPPHHHHHHPH
PHPPPPHPHHHPHPHHHHPHHPHHPPPHPHPPPHHHPPHHPPHHPPPH
PHHPHHHPHHHHPPHHHPPPPPPHPHHPPHHPHPPPHHPHPHPHHPPP
PHPHPPPPHPHPHPPHPHHHHHHPPHHHPHPPHPHHPPHPHHHPPPPH
PHHPPPPPPHHPPPHHHPHPPHPHHPPHPPHPPHHPPHHHHHHHPPHH

Instances S

HHHHPHHHHHHPPHHPHHHHHHHHPHHPHHHHHHHHHHPPHHPPPPPHHPHHHHHHHHPHPPHHPPPHHHHHHHHPHHHHHHPPHHHHHHHPHPPHHHHHHHHHPPHHPPPHHHHHHHPHHPHHHHHHHPPHHHH
HHPPHPHHHHHHHHHHPHPPPPHHHPPPHHHHHPPHHHHHPPHHHHPPHHHHPPHHHHHHPHHHHPPPHHPPPHHHHHHHHPHPPHHHPPPHHHHHPPHHHHHHHPPPHHPPHHHHHPPPHHHHHHHHHPHPPHHHHHHHPPPHHHPPHHP
HHHPPPHHPHHPPPPPHHHHHHHHPHPPHHPHHPHHHHHPPPHHHHHHHHHPPHPHPPHPHPPHHHPHPPHPHPPPHHHHHHPHHHHPPPHHHPPPPHHPPPHHHPPHHHHPHHHHHPPHHHHHHPPPHHHHHHPPPHPPHHHHPHHHHHHHPPHHPPHHH
HHPPHPHHHHHHHPPHPHPPHPHPPPPHHHPPPHHPHPHHPPHHHHHPPHHHHPPHHHHPPHHHHHHPHHHHPPPHHPPPHHHHHHHHPHPPHHHPPPHHHHHPPHHHHHHPHPPPHHPPHHHPHHPPPHPHHHHHHHPHPPHPPHHHHHHPHPPPHHHPPHHP

Instances R

PPPHPHHPHHPPPHPHPPPPHPHHPPHPHHHHHPPHHPPHHHHHHPPHPPHHPPHPHPHHHHHPHHPHHHPPPHHHPHHPPHPHPPHPPPHPPHPPHPPHHHPHHHPHPPHPHHPHHHHPHPHHHPHHHPPPPPPHHHHHHPPPPPPPPHHHPPHPHPPPHPHPHPHHPPHHPPPPHHHHHHPPPHHPPPPPHPPPHHPP
HPHHPPHPPPPPHHPHPHPHHPPHPPPPHHHHHHPPPHPPHHHPPHPPPPHHPPHHHPHPHHHPPHPHHPPHPHHPPPPHHPPHPPHHHHPPPPPHHHPPPPHPPPPPPHPPHHPHHHHPHHHHHHHHPPHHPPPHPHHHPHHHHHPHHPHHHPHPHHPPPPHPHHPHHHPHPPPPHPPPPPPHPHHHHHPHHPPPHPPH
HPHHHPHHPHPHPPPHHHHHPHPHPHHHHPPPHHPPPPPPHHPPPPHPHHHPPPPHPPPHHPHHPPPHPPHPPPHHHHPHHPHPPPPHHPPPHHPPHPPPHPPHHHPHHHPHPPHPHHHHPPHHPPPPHHHPHHPPHPPHHHHPPHPHPPHPHPPPPPHPHPHHHHHHHPHPHHHHHHPHHPPPPHPPPPHPPPHHHPHH

Instances F90

PPHHHPPPHHPPPPHHPHHHHHHPHPHPHHPHHHHHPHHHPHPHHHHPHHPPPPHHHPHPHPPHHHPHHPHPHPPHHHPPPPHHPPHPPP
PHHPPHPHHPHHHPHHHPPHHHHHHPPHPHPPPPHHHPHPPHHHHPHHHHPHHHPHHPPPPPHHPPPPHPHPHPHPHHPPHHHPPPHHHP
HPHPHHHPHHHHPHHHPPPHPPPHPPPPHHHPPHPPPPHHHPPPPPPPPHPHHPHHHHPHHHPHPHHPPHHHHHPHHPPHHPHHHHHHPH
PHHHPPHPPHPHPPPPHPPPHPHPPHPHHPHPPPHHHPHHHPPHHHPPHPPPPHPHHHPPHHPPHHHPPHHHHHHPHHHHHHHPHHHHPH
PPPHPHHHHHHHPPPHPPHHHHHPHHPPHHPPHHHHPHPHPHHPPHHPPPPHPPPHHHPHPHHHHHHHPHHPHPPHHPPPHHHPHPPHPP

Instances F160

HHPPHHHHHPHHHPPPHHHPPHHHPHPPHHHHHPPPHHHPPPHPHHPPPPPHHPPHHPHHPHPHHPPPPPHHHPPPPHPHHHPPHPPPHHHPHHHHPPHHPHPHHHHPHHHHPPHHPHHPHHPHHHPHPPHPHHPHPHHPHHHPHHPPHPPPHPPPPPPPHHHPHHHHHPHHHHHPPHPP
PHHPHPPPHPPHHPHHHPHPHHPHHHPHHHPPPHHPPHPHPHHPHHHHPPHHPHPHHHHHPHHPPPPHPHPHPPHHHHPHHHHPHHHHHPPHPHHHPPPHPHPPHHPPPHHPHPHPPPPPHPHHPHHHPHPPPPHHPHHHHHPPPHHHHHHHHPHHPPPPPHPPPHPPHPPPHHPHHHHH
HHHPHPPHHPPPHPPPHPHPHPPHHHHPPHHHHHHPHPHHPPPPPHPPHHPHHHHHHHHHHHPPHPPHPPHHHHHHHHPPPPHPPHHHHHPPHHHPPHHPPHHHHHPPPHHHHHHPHHHPPPHHPPHPPPHPPHPPPHPPPPHHHPPHHPHPPHHHPHHPPHHPHHPHPHPHPHPHPHHP

Predictions for Harvard instances

Will's H-core threading

Tabu plus LNS

Miscellaneous

HarvardInstances.tar: Tar file of Harvard Instances.
seq.txt: Text file of sequence families: Harvard, R,S,F90,F160.
altschulEriksonDinuclShuffle.py : Our implementation of Altschul-Erikson dinucleotide shuffle algorithm. WARNING: To use in context of HP-sequences, change 'H' to 'C', 'P' to 'G', apply Altschul-Erikson algorithm, then change 'C' to 'H', 'G' to 'P'. Thus one must use the program driverAltschulEriksonForHPmodel.py.

Benchmarks for Will's H core threading program

Small examples for use of Will's code:

HPstruct -help

HPstruct -seq=HPPPHPHHHPPHHHHPHPHHPHPH -lat=FCC -maxSol=1 -dbPath=/cluster/data/CPSP_CoreDB

HPstruct -seq=HPPPHPHHHPPHHHHPHPHHPHPH -lat=FCC -allBest -dbPath=/cluster/data/CPSP_CoreDB

HPconvert -help

HPconvert -m=a2p -str=BDRUBLRDRDBLFLFLLURUBDBLBRFRBDFLBLRDFRRDFUFLRDBLBLFUBLLUFDRUFLFDBRFRFULDBURUFRBRBDFDLUFDBDBLFL -lat=FCC 


Exectubles,libraries and include files are in

/usr/local/bin
/usr/local/lib
/usr/local/include

Randomized Data

These sequences were created by using the Altschul-Erikson dinucleotide shuffle algorithm to create sequences having the same diresidues (not simply the same expected diresidue frequency, which latter can easily be constructed by a first-order Markov chain).

LS+LNS (Local Search plus Large Neighborhood Search Results: For the randomized F90 instances, randomized F90-double instances, and randomized F180 instances, this file gives the
Randomized F90 Instances
Randomized F90-double Instances
Randomized F160 Instances
Randomized F60-double Instances

Programs to randomize HP-sequences using Altschul-Erikson dinucleotide shuffle

analyze.py: miscellaneous program to massage and analyze output of cluster runs of Will's program.
README
dataRandomized.txt
run.py: Program to launch torque cluster computation with bound of 30 minutes of Will's program.