Biomacromolecular channels and pores play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity. MOLE 2.0 is an advanced software tool, which has been designed to analyze molecular channels and pores. Benchmark tests against other available software tools showed that MOLE 2.0 is by comparison quicker, more robust and more versatile. As a new feature, MOLE 2.0 estimates physicochemical properties of the identified channels.
SiteBinder is an application for superimposing of multiple protein structural motifs (binding sites, secondary structure elements, etc.) and creating their 3D models. Superimposition is calculated via quaternion algebra and optimal pairing of atoms is searched in parallel. The software provides a user-friendly and intuitive interface and allows to select, which atoms will be included into calculation.
Nemesis is an advanced molecular structure builder. It is able to build a molecule from predefined 3D fragments. Molecules can be visualized in several representations, including monoscopic and stereoscopic. The geometry of the built molecule can be easily measured and manipulated. Nemesis is a modular program, and its functionality can be extended by using various plugins. For example, it supports imports and exports of various chemical formats using the OpenBabel library. This library is also used for geometry optimization by several force fields.
PMFLib is a set of various programs and libraries suited for free energy calculations by means of potential of mean force methods (PMF). It currently implements the following PMF methods: adaptive biasing method, constrained dynamics, metadynamics, restrained dynamics, and the string method. The sampling can be improved by using the multiple walkers approach in conjunction with the adaptive biasing method and metadynamics. Replica exchange molecular dynamics can be used to further improve the sampling. The library implements various advanced reaction coordinates, which can be easily combined together via several operators.
MotiveValidator is a platform for a set of applications designed to help you determine whether a residue or a ligand in a biomolecule or biomolecular complex is structurally complete and correctly annotated according to its models stored in the wwPDB Chemical Component Dictionary (wwPDB CCD).
EEM SOLVER and ABEEM SOLVER
Electronegativity equalization methods (EEM) are one kind of fast approaches for charge calculation. These methods (based on DFT) are the alternative to calculation of charge distribution using ab-initio methods. EEM are significantly faster than ab-initio methods and their accuracy corresponds to ab-initio methods. In the project, we first implemented two equalization methods: classical EEM and its extension ABEEM (atom-bond EEM). Then, we optimized and parallelized our code and obtained very effective program for charge calculation. After it, we performed parameterizaton of the EEM (with the STO-3G basis set and Mulliken population analysis) for large sets of organic, organohalogene and organometal molecules. Next steps will be: a parametrization of the EEM for bigger bases and other population analyses, a parameterization of ABEEM method, a utilization of EEM and ABEEM charges in computational chemistry simulations, etc..
The program TRITON is graphical tool for modelling protein structures and their properties. It can be used for modelling protein mutants based on the wild type structure by homoly modelling using the external program MODELLER. Subsequently, properties of these protein mutants are modelled.
Knowledge of conformational behavior of molecules plays an important role in drug design and it could help in description of interested phenomena in chemical behavior of molecules. The program based on single-coordinate-driving (SCD) method called CICADA has been developed in our laboratory. The ability of the CICADA program in conformational search was tested on large sets of molecules included amino-acids, hydrocarbons, nucleic acids bases, carbohydrates. The search in torsion angle space was extended to systematic docking procedure. The new method was tested on docking of small organic molecules into the cyclodextrine molecules. Used SCD method allows parallelization with large scale factors. New parallel version of the CICADA program was developed recently and is tested on large scale of molecules. The programs for consequential analyses (splitting into conformational families, calculation of geometrical parameters) are also developed. The graphical interface to CICADA program based on WWW server is under development.