HPview allows for the interactive visualization of lattice protein structures in the HP-model.
The structure has to be given in absolute move string representation.

If the sequence is given too, a colored visualization is given.

**Introduction**

# When using HPview 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.

Results are computed with HPview version 2.4.6 linking Gecode 1.3.1

**Overview**

The following parameters are used to control the execution of HPview

Furthermore, additional information is available

# Input

## Structure

The structure to visualize given as an absolute move string.
It can be either a backbone-only or a side-chain model structure.

Absolute move strings are a compressed string representation of structures in lattice protein models. Here the lattice specific neighboring vectors between successive monomers are described instead of their exact coordinates. Thus all possible vectors are uniquely encoded. Their number depends on the lattice.

Encodings used by the CPSP-tools:

Note that we use a two-letter encoding in the face-centered-cubic (FCC) lattice. This was done to allow for an intuitive readable notation since all neighboring vectors in FCC are a combination of two standard 3D-cubic directions. The encoding follows the description in the order of X-, Y-, Z-changes to get a unique encoding.

Absolute move strings are a compressed string representation of structures in lattice protein models. Here the lattice specific neighboring vectors between successive monomers are described instead of their exact coordinates. Thus all possible vectors are uniquely encoded. Their number depends on the lattice.

Encodings used by the CPSP-tools:

Vector | Move | Vector | Move | ||

3D-cubic | (+1,0,0) | F | 3D-FCC | (+1,+1,0) | FR |

(-1,0,0) | B | (+1,-1,0) | FL | ||

(0,+1,0) | R | (-1,+1,0) | BR | ||

(0,-1,0) | L | (-1,-1,0) | BL | ||

(0,0,+1) | U | (+1,0,+1) | FU | ||

(0,0,-1) | D | (+1,0,-1) | FD | ||

(-1,0,+1) | BU | ||||

(-1,0,-1) | BD | ||||

(0,+1,+1) | RU | ||||

(0,+1,-1) | RD | ||||

(0,-1,+1) | LU | ||||

(0,-1,-1) | LD |

Note that we use a two-letter encoding in the face-centered-cubic (FCC) lattice. This was done to allow for an intuitive readable notation since all neighboring vectors in FCC are a combination of two standard 3D-cubic directions. The encoding follows the description in the order of X-, Y-, Z-changes to get a unique encoding.

The parameter constraints are: String length has to be in range (1,300). Maximally 1 line is allowed. Only [UDLRFB]* absolute move strings are allowed for specification.

Defaults to ()

Defaults to ()

## Sequence

The HP sequence of the molecule to visualize (optional).
If provided, a colored 3D rendering is generated. The current
coloring scheme is

The parameter constraints are: String length has to be in range (1,300). Maximally 1 line is allowed. Only the HP alphabet is allowed for specification.

Defaults to ()

Defaults to ()

## Lattice

The 3D-lattice model to use for optimal structure calculation. Currently, HPview supports the

- CUB : Unrestricted 3D-cubic lattice
- FCC : Unrestricted 3D face centered cubic lattice

# Output Description

The HPview webserver does an instant 3D rendering of the given lattice
protein structure using glmol.

In addition, the PDB file used for rendering is given for download and inspection.

In addition, the PDB file used for rendering is given for download and inspection.

# Input Examples

## Backbone-only structure with sequence

Exemplifies the input of a backbone-only structure with an according sequence in the cubic lattice.

## Backbone-only structure in FCC

Exemplifies the input of a backbone-only structure in the FCC lattice.

## Side-chain structure in FCC

Exemplifies the input of a side-chain structure with an according sequence in the FCC lattice.