Molecular Visualization with Supports of Interaction, Immersion, and Collaboration among Geographically Separated Research Groups

Molecular Visualization with Supports of Interaction, Immersion, and Collaboration among Geographically Separated Research Groups

Moacyr Francischetti-Corrêa (Universidade Federal de São Carlos, Brazil)
DOI: 10.4018/978-1-4666-3667-5.ch017
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Abstract

In the search for new drug and medication discovery, especially related to drug-receptor interaction, the importance of interaction among researchers is essential, either within the same room or dispersed throughout the world. The interaction in an online environment through the molecule shared view and information and ideas exchange via text and/or voice enable researchers to discuss molecule aspects under study, increasing the chances of reaching the new compound’s identification. In subsequent sections an architecture that uses concepts of Distributed Multiuser Virtual Reality, Computer-Supported Collaborative Work, and world-wide network communication techniques for creating a high performance system that allows real-time interaction among various geographically dispersed research groups studying molecular visualization and using hardware systems ranging from desktop to immersive systems as CAVEs is presented. Its construction was made possible by defining a structure based on local servers to each group, which communicate with each other on a remote network, and creating a protocol for communication among these servers that seeks agility to minimize the negative effects of packet loss and delay delivery, Internet characteristic problems.
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Introduction

In Medicinal Chemistry, it is needed to have great knowledge in organic chemistry, pharmacology, physics, biology, medicine, and docking studies supported by computer, everything at once. It means having a multidisciplinary environment, and it almost never happens in a single Department, Campus or even in cities. Therefore, there is a great need of creating a collaborative atmosphere among geographically separated research groups so they can research structures, properties and molecular dynamics, quickly, without necessarily need to be together in person.

Francischetti-Corrêa (2010) describes a high performance architecture created in order to make possible the cooperation among geographically-separated research groups, in the molecular view context. The differential of this architecture, when compared with other existing systems, is that it gave importance to communication problems on the internet and tried to improve the collaborative experience among users linked up thereby, so they can interact in a single environment in a compatible time with its application, with the possibility of using virtual reality resource with multiprojection.

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Background

Material and computational molecular models are instruments that assist researches and the teaching chemistry process. Material models have been used for over 120 years to represent physics laws that rule chemical structure and processes. Models and computer simulations replaced virtually all of it material models as essential tools for refining and analysis of experimental data.

In the mid-1960 Cyrus Levinthal created the first Interactive Molecular Visualization System (IMVS) (Levinthal, 1966). This program enables a user to modify the movement and molecule orientation by using a precursor of a primitive track-ball device. With this device it was possible to set menu items, choose an object or zoom important parts of the molecule. The visualization was only from what we call nowadays sticks, that represent the bond between the atoms.

From that time on, many other Interactive Molecular Visualization Systems (IMVS) were developed, some of them using immersive and/or collaborative technologies. As each computing technology breakthrough has arisen, it was incorporated by some IMVS. Nowadays the interactive molecular visualization system innovations are focused to the interface between scientists and molecular model, where virtual reality is used to produce a strong link between the user and the molecular model.

It is possible to investigate computationally the structure, properties, and dynamics of complex molecular systems that include million or billion atoms by using molecular visualizers, which are programs that can read the molecular structure and its properties from files created from experiments or theory, showing them in tridimensional models. It is possible to view structures in different styles; the most commons are ball-and-stick and space filling spheres. The user can, yet, interactively to rotate the molecule, zoom it, estimate the distance between atoms, estimate angles, adjust rendering parameters, besides allowing stereo viewing, estimate and show molecular properties, electrostatic interactions, atomic volumes and molecular orbitals, among other resources.

Beyond software designed to the visualization of molecules, there are still the ones created to molecular modeling, with two general approaches: application of quantum theory and molecular mechanics. Quantum theory is strict and computationally intensive. Molecular mechanics uses Newtonian mechanics and classical electrostatic to describe the physical base behind of molecular models in which atoms are defined like points of charge with associated mass. The mechanical molecular methods can be applied to calculate static molecular structures that represent minimum energy set by the atomic distances, link angles, and torsion angles. Molecular modeling process is defined by the problem’s complexity to be solved and by the computational availability resources needed to realize such task. However, depending on the size of the problem, the solution can last days or even weeks to be found using a personal computer. This simulation can be done in a computational grid, what decreases the spent time, but nevertheless the process is very far to be a real-time demonstration.

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