CPSP-Tools Server
HPview - Help
BIF
IFF

Introduction

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.

When using HPview please cite :

Results are computed with HPview version 2.2.2 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:

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.

?  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.

?  Lattice

The 3D-lattice model to use for optimal structure calculation. Currently, HPview supports the
Unrestricted means that the structures are not restricted e.g. to a compact cube as done by other approaches.

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.

Input Examples

?  Backbone-only structure with sequence

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

?  Side-chain structure in FCC

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

?  Backbone-only structure in FCC

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