There are two molecular processes that are essential for living bodies to maintain their life: the molecular recognition, and the self-organization or self-assembly. Binding of a substrate by an enzyme is an example of the molecular recognition, while the protein folding is a good example of the self-organization process. The two processes are further governed by the other two physicochemical processes: solvation and the structural fluctuation. In the present article, the studies concerning the two molecular processes carried out by Hirata and his coworkers, based on the statistical mechanics of molecular liquids or the RISM/3D-RISM theory, are reviewed.

We have made a stereoscopic viewing system for a large assembly of proteins using OpenRasmol. The stable version 2.7.1 of OpenRasmol is modified for the system, which uses an eye-ware instead of trained bare-eyes. Software rendering and other benefits in OpenRasmol are reserved. A 3-D graphic board is used just for the active stereo method, not for the acceleration of rendering. Our modification is simple one. In the results, an actin filament of 16-mers, where one actin monomer has about 400 residues, in space filling model can be rendered in stereoscopic viewing mode and can be made one turn within 10 seconds as quick as non-stereoscopic mode. Other 3-D molecular graphics programs with 3-D accelerator boards cannot render such a large assembly of molecules in stereoscopic usage mode as quickly as the modified OpenRasmol. An attractive application of our system is stereoscopic viewing with a large 200 inch screen in passive stereo method. Simultaneous usage is available for more than 100 persons with inexpensive eye-wares. The large screen allows us to investigate an interior of a groove in an actin filament in detail. Our modified OpenRasmol is distributed following the license, RASLIC, as an open source code at our web site (www.irisa-lab.bio.kyutech.ac.jp/openrasmol), where video files showing rendering speeds of our modified OpenRasmol are also available.

Researchers studying biomolecules require easy-to-use, customizable tools allowing them to effectively use other molecular science packages written for molecular dynamics (MD), quantum chemistry, statistical mechanics, and molecular graphics. This paper presents a Scala tool for the computational science of biomolecules (STCSB) developed in Scala, which allows users to prepare and run MD simulations, as well as perform three-dimensional reference interaction site model (3D-RISM) calculations of biomolecules. Features of the STCSB include the following: (1) a cross-platform application running on a Java virtual machine; (2) handling hierarchical XML-based data formats such as the protein data bank markup language (PDBML); (3) prepared application programming interfaces (APIs) with both character user interface (CUI) and graphical user interface (GUI) options; (4) prepared APIs for molecular graphics; and (5) a scalable source code based on the Model-View-Controller (MVC) architectural pattern.