Input and runtime details for job 2517422 (precomputed example)

Input

	HP sequence		PPHHHPHPHHPHPPPPHHHPHPHHPPPPPHHHPP
	Lattice		Unrestricted 3D face centered cubic (FCC)
	Structure Model		backbone-only model
	Allow symmetric structures		no
	Number of Structures		10
	One representative per equivalence class		yes

Job ID 2517422 (server version 4.2.2)

	Job Submitted & Queued		@ Mon Jun 13 17:32:37 CEST 2016
	HPstruct Started		@ Mon Jun 13 17:32:40 CEST 2016
	HPstruct Finished & Post-Processing		@ Mon Jun 13 17:32:40 CEST 2016
	Job Completed		@ Mon Jun 13 17:32:41 CEST 2016

DIRECT ACCESS: http://cpsp.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=2517422&toolName=HPstruct ( 30 days expiry )

Description of the job

backbone example

Exemplifies the prediction of optimal backbone-only lattice protein structures within the FCC lattice that show different placements of their hydrophobic residues, i.e. they are representatives of the according equivalence classes.

Output download complete results [zip]

List of optimal structures for input sequence PPHHHPHPHHPHPPPPHHHPHPHHPPPPPHHHPP within lattice FCC.

Minimal energy for any structure is -40.

Energy level

Energy
-40	FLLUBUBUBDFRBDFLFLRDRUBRLDBLLUFUFUFRBURDFRLDBRBURDFDFLFLLUBLBLBDRD	FLBLBUBUFURDFULDLDFRBRRUFLLUBLBDBDRDBUFRRDFLRUBULUBLFLLDFDRDRDFRBR	FLLUBUBUBRFDBLFDFLRDRUFRFLLDLUBUFRBUBURDFRLDBRBDLDBULDLUFUFLRUBUBD	FLLUBLBLBRFDBRFUFURDLDFDFURULUBLFDBLBLRDFDRUBDBRFRBUBULUFLFLRUBRRD	FLLUBUBUBDFRBDFLFLRDRUFRFLLDLUBUFRBUBURDFRLDBRBDBULULUFLFDLDBRBDFD	FLLUBUBUBDFRBDFLFLRDRUFRFLLDLUBUFRBUBURDFRLDBRBDBULULUFLFDBDFLBDBR	FLLUBUBUBDFRBDFLFLRDRUFRFLLDLUBUFRBUBURDFRLDBRBDLDBLFLLUFURUBDBDLU	FLLUBUBUBDFRBDFLFLRDRUFRFLLDLUBUFRBUBURDFRLDBRBDLDBLLUFLFUBRFUBUBD	FLRUFUFUFLBDFRBDBRLDLUFLBDBUBRRUFRLUFULDBLRDFLFUFDRDRDRUBUBRLUFUFD	FLRUFUFUFDBLFDBRBRLDLUFLBDBUBRRUFRLUFULDBLRDFLFUFRFDRDBRBUBURDFDLD

Select energy level: -40

Visualization of structures for selected energy level

This visualization is created with glmol using the color coding 'grey' = H, 'blue' = P, 'yellow' = backbone in side-chain models.

PDB representation of the shown structure Download PDB-File

Job resubmission

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When using HPstruct please cite :

Martin Mann, Sebastian Will, and Rolf Backofen
CPSP-tools - Exact and Complete Algorithms for High-throughput 3D Lattice Protein Studies.
In BMC Bioinformatics, 9, 230, 2008.
Martin Mann, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will, and Rolf Backofen.
CPSP-web-tools: a server for 3D lattice protein studies.
Bioinformatics, 25 (5), 676-677, 2009.
Martin Mann, Rolf Backofen, and Sebastian Will.
Equivalence Classes of Optimal Structures in HP Protein Models Including Side Chains.
Proceedings of the Fifth Workshop on Constraint Based Methods for Bioinformatics (WCB09), 2009.
Rolf Backofen and Sebastian Will.
A constraint-based approach to fast and exact structure prediction in three-dimensional protein models.
Journal of Constraints, 11 (1), 5-30, 2006.

Results are computed with HPstruct version 2.4.6 linking Gecode 1.3.0 and BIU 2.3.6

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