An interactive 3D viewer of molecules compatible with the suite of ANTHEPROT programs

doi:10.4236/jbpc.2012.31004

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Vol.3, No.1, 35-38 (2012) Journ al of Biophysical Chemistry

http://dx.doi.org/10.4236/jbpc.2012.31004

An interactive 3D viewer of molecules compatible

with the suite of ANTHEPROT programs

Gilbert Deléage

Unité Bases Moléculaires et Structurales des Systèmes Infectieux, UMR 5086 CNRS, Université Claude Bernard Lyon 1, Lyon,

France; [email protected]

Received 11 October 2011; revised 3 December 2011; accepted 17 December 2011

ABSTRACT

In this p aper, I will describe a completely ne w 3D

module which can be called from within the well

known ANTHEPROT program devoted to protein

sequences analysis. This module allows fully

interactive handling of high-quality 3D struc-

tures with various modes of representation (CA

sticks, wireframe, ball and sticks, spacefill mod-

els as well as surface, ribbons, Ramachandran

plots). Alternatively, ANTHEPROT 3D can be

used as an external program fully independant

from the global package. It is available from the

download page of the web site

(http://antheprot-pbil.ibcp.fr/). More than 2800

downloads last year were recorded since the

program was delivered.

Keywords: Protein; Sequence Analysis; Structural

Bioinformatics; Software; 3D Structures

1. INTRODUCTION

Many programs [1-7] or Web servers [8-10] exist for

the visualisation of th e 3D structure of protein s. Howeve r,

few of them have some possibilities for sequence analy-

sis [7,11]. In the 90’s, we have proposed one of the very

first package for the analysis of protein sequence [12].

For over 20 years, this software has been continuoulsy

updated for various plateforms including Apple II, Mac-

Intosh, DOS [13] and AIX (IBM unix) operating system

in the 1990’s [14-16]. In the latest published version,

which is designed for the Windows OS, several im-

provements were made such as the addition of a client-

server mode [17] for distant submissions that takes ad-

vantage of remote servers hosting databases regularly

updated [18]. However, at that time, no effective 3D

module was associated with the program.

In this article, I describe a completely new version of

the program ANTHEPROT 3D that allows interactive

manipulation of 3D structures of proteins. The program

is mainly devoted to th e comprehensive understand ing of

biological molecules by viewing their 3D structures. It

includes all the standard functions found in other 3D

viewers. The main originality is that it can be launched

directly from the main window of the widely used AN-

THEPROT program designed for the analysis of protein

sequence. A gallery showing the possibilities of this

module is available at http://antheprot-pbil.ibcp.fr/3D.

2. SYSTEM AND IMPLEMENTATION

ANTHEPROT 3D program is a completely new pro-

gram for Windows interface, which uses the OpenGL 3D

library. So, the program performs best on computers that

have OpenGL graphic cards but also works on any card

(in a quite performant emulation mode). The program is

available, as a complete ready-to-run archive file. An

help file (ANTHE.HLP file) is also present in the pack-

age. The program can also be considered as an interface

for several well known external programs, such as the

MSMS molecular surface for surface calculation [19],

the ribbon molscript program [20], the DSSP program for

secondary structure calculation [21], the DELPHI algo-

rithm for electrostatic potential calculations [22] and

“REDUCE” program for hydrogen additi on/rem oval [23] .

3. MAIN FEATURES

ANTHEPROT 3D consists of 4 different panels (Fig-

ure 1). The first one (Figure 1(a)) is the OpenGL win-

dow for the graphical display. The manipulation of the

molecule can be achieved by a trackball emulation mode

that can be activated or deactivated in real time. This

feature allows a very precise manipulation of the mole-

cule or, alternatively, the discovery of the molecule with

a flying mode. Once a PDB file is loaded, the secondary

structures are calculated on the fly using the DSSP algo-

rithm [21], the CA trace is shown in this window as

sticks colored by chain (default). Two other related win-

dows are displayed: one (Figure 1(b)) is used to provide

a list of amino acids from which the selection of the

esidues can be made in a multiple selection mode. The r

G. Deléage / Journal of Biophysical Chemistry 3 (2 012) 35-38

(c)

(d)

(a)

(b)

Figure 1. Program main interface. (a) The main window for viewing molecule (pdb code: 3SGB). The electrostatic potential is dis-

played (positive potential in blue and negative one in red) onto the MSMS surface; (b) The window amino acid list for selection; (c)

The information window; (d) The Ramachandran window. An arrow indicates the current position in the sequence.

third window (Figure 1(c)) is used to provide the user

with useful information (distances, angles, global content

in secondary structure, phi/spi angles, sequences, number

of chains, number of atoms). The program is fully cus-

tomisable for color codes (amino acid groups, chains,

atoms, hydrophobic/hydrophilic residues, B factor, elec-

trostatic potential) that can be combined with conven-

tional modes of representation (CA backbone, wireframe,

sticks, ball and sticks, spacefill, ribbons and surface).

The graphics quality can be adjusted so as to provide a

good compromise between quality and speed of execu-

tion depending upon the molecule size and the type of

graphic card.

The program allows the display of large molecules.

Indeed, Figure 2 shows the surface of a viral capsid

(2BUK), rendered in a solid Gouraud mode, colored by

subunits. It should be noted that even in this mode, the

interactivity is preserved. Alternatively, the grid surface

can be calculated and the transparency of the surface can

be adjusted with a slider. This surface can be still interac-

tively handled on a machine equiped with graphic cards

supporting OpenGL. ANTHEPROT can display onto the

MSMS surface the electrostatic potential calculated by

using the external program DELPHI. The manipulation

of the molecule in the graphics window is still fully in-

teractive using a virtual trackball for rotation, zooming

and moving. Moreover, the program has selection capa-

bilities through the picking of atoms for identification of

parent residues, distance between atoms, angles and tor-

sion angles.

ANTHEPROT 3D also offers a selection mode of

amino acids within a sphere, the radius of which can be

adjus ted on the fly by the user. The f ar and near clipping

plans can also be interactively adjusted. An interactive

Ramachandran plot is also available (Figure 1(d)) which

allows to display the phi, psi angles, the list of angles and

an panel showing the corresponding sequence and sec-

ondary structure. This panel can be updated after picking

a point in a region of the Ramachandran surface or

moved backward or forward by using the arrows of the

G. Deléage / Journal of Biophysical Chemistry 3 (2 012) 35-38 37

Figure 2. MSMS surface rendering in ANTHEPROT 3D view-

ing program. Pdb code: 2BUK (from the biological unit file

from PDB).

keyboard. In all cases, both sequence and secondary

structure around the current position is updated. This

original tool is very useful to connect the sequence of a

protein, its secondary structure and the 3D display. For

example, when a PDB file is loaded from within the pro-

gram for protein sequence analysis, the sequence of the

protein is automatically extracted and provided in the

sequence module. This allows to enter into this sequence

program from a 3D structure. So, the ANTHEPROT 3D

can be considered as an optional module to the classical

ANTHEPROT program.

Another useful tool is the complete support of interac-

tive multiple stereo views. Among the supported modes,

the classic mode with two views side by side (crossed

eyes), the anaglyph red/green stereo mode, the quad-

buffer mode which needs polarized screen and passive

glasses, and the interlaced row mode suitable for flat

screens such as stereo Zalman.

Some examples of several kinds of representations of-

fered by ANTHEPROT 3D are given in Figure 3. More-

over to take advantage of the important functions pro-

vided by other programs, ANTHEPROT 3D is able to

launch some external programs, transparen tly to the user.

For the display of ribbons (Figure 3(b)), ANTHEPROT

3D is able to generate input files for Molauto/MOL-

SCRIPT and it is able to exploit the output files gener-

ated by these two programs. Helices can be shown in

“cartoons” mode (alternatively helices can be represented

as cigars that give their N and C orientations). The addi-

tion/suppression of hydrogens is performed by using a

(a)

(c)

(b)

(d)

Figure 3. Examples of views obtained with ANTHEPROT

3D. (a) Alpha carbon view of 5HMG in colored subunits;

(b) Moscript view of 1MAX; (c) Spacefill colored atom

view of hydrogenated 1MBJ; (d) Transparent grid surface

of 1CRN.

call to the “REDUCE” program (Figure 3(c)). Surface

calculation can be performed in a fully transparent man-

ner with the help of the widely used MSMS algorithm

(Figure 3(d)).

The program can also generate video recording from

the assembly of regularly dumped images. In order to

illustrate the capabilities of the program a gallery web

site is visible at http://antheprot-pbil.ibcp.fr/3D.

4. DISCUSSION

Although many 3D protein viewers exist, to my know-

ledge, ANTHEPROT is the unique program that was

primarily devoted to protein sequence analysis (with a lot

of tools such as matrix dot-plot, multiple alignements,

secondary structure prediction) that also allows a power-

ful rendering of the 3D structure of protein. That is why

this completely new 3D module was written in order to

allow 3D structure handling from within the ANTHE-

PROT sequence software. As a consequence, it should

not be considered as a additional modelling tool but

rather as a vizualisation tool coupled to a sequence ana-

lysis program. Efforts have been made in order to facili-

tate the discovery of proteins organisation through the

CA default mode. In this context, the user-friendly inter-

face has been enhanced by the implementation of a

G. Deléage / Journal of Biophysical Chemistry 3 (2 012) 35-38

[11] Li, W.Z. and Godzik, A. (2006) VISSA: A program to

visualize structural features from structure sequence ali-

gnment. Bioinformatics, 22, 887-888.

doi:10.1093/bioinformatics/btl019

trackball mode which allows an efficient “flying mode”

to watch the 3D structure. Efforts were also made to

simplify the first use of the program. It is simple and

intuitive enough for use by any user without the n eed for

experience in the program or in-depth knowledge of the

3D structure of proteins. The ANTHEPROT 3D program

is freely available and, during the last 12 months 2888

downloads of the software have been registered. Possible

developments include a specialisation of the module to-

wards protein interaction interface visualisation and ana-

lysis.

[12] Deleage, G., Clerc, F.F., Roux, B. and Gautheron, D.C.

(1988) Antheprot: A package for protein-sequence analy-

sis using a microcomputer. Computer Applications in the

Biosciences, 4, 351-356.

[13] Deleage, G., Clerc, F.F. and Roux, B. (1989) Antheprot:

IBM PC and Apple macintosh versions. Computer Appli-

cations in the Bioscie nces, 5, 159-160.

[14] Geourjon, C., Deleage, G. and Roux, B. (1991) Antheprot:

An Interactive graphics software for analyzing protein

structures from sequences. Journal of Molecular Graph-

ics, 9, 188-190. doi:10.1016/0263-7855(91)80008-N

5. ACKNOWLEDGEMENTS

Thanks are due to Dr. Ramon Yáñez López (University of Barcelona)

for providing me some pieces of code for centering molecule and to

CNRS and Lyon University for supporting this work.

[15] Geourjon, C. and Deleage, G. (1995) Antheprot: A soft-

ware to display and analyze 3d nmr structures. Journal of

Trace and Microprobe Techniques, 13, 337-338.

[16] Geourjon, C. and Deleage, G. (1995) Antheprot-2.0: A

3-dimensional module fully coupled with protein-seq-

uence analysis-methods. Journal of Molecular Graphics,

13, 209-212. doi:10.1016/0263-7855(95)00035-5

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