LCC

Laboratory of Computational Chemistry

MUNI CEITEC SCI NCBR

We, at the laboratory of computational chemistry, engage in the development of our own software. This software is used for faster and/or more reliable calculations, or the evaluation of system properties that are not available by conventional methods and tools. Some of the developed software is also available to other researchers.
CATs

CATs

The package CATs contains several utilities for AMBER topology and coordinate manipulation. Operations can be performed on the whole structure or on a subset defined by a mask. The mask syntax is compatible with the AMBER mask syntax, and additionally it contains several extra selection operators. Parallel processing of AMBER trajectories is supported, together with a simple collection of the results scattered throughout the output files. The package also contains a simple scripting environment that can combine several individual tasks in a more complicated fashion, including cycles and conditional structures.

Infinity

Infinity

Infinity is a complex environment intended to simplify the management of computational jobs. It consists of two subsystems: AMS and ABS. The Advanced Module System (AMS) manages the installed scientific software. It simplifies the selection of the suitable build of the installed software by taking into account host architecture and available computational resources. The Advanced Batch System (ABS) is an extension of the Torque batch system. It simplifies job submission, encapsulation of job data transfer between the host computer and computational nodes. It also archives all information about a job spanning the entire job life-time. It supports advanced jobs called collections.

NEMESIS

NEMESIS

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.

QSPR Designer

QSPR Designer

QSPR Designer is a modular and easily extensible software, which allows us to automate the process of QSPR model design and evaluation. The software can read or calculate structural properties of molecules, employ them as QSPR descriptors, effectively design and parameterize QSPR models, predict physicochemical properties of molecules and evaluate the models.

TRITON

TRITON

The program TRITON is a graphical tool for protein engineering, docking and enzymatic reaction modeling. It can be used to model protein mutants by homology modelling. Enzymatic reactions are modeled using semi-empirical quantum mechanical methods. The molecular docking methodology is used to study the binding properties of protein-ligand complexes. The program TRITON offers graphical tools for the preparation of input files and for the visual analysis of output data.

EEM Solver

EEM and ABEEM Solvers

EEM Solver and ABEEM Solver are programs for calculation of partial atomic charges via the Electronegativity Equalization Method (EEM) and Atom Bond Electronegativity Equalization Method (ABEEM). The calculation of charges is very fast and their accuracy is comparable with ab-initio quantum mechanical methods.

MOLE

Mole

The program MOLE is a universal toolkit for rapid and fully automated location and characterization of channels, tunnels and pores in molecular structures. The core of the MOLE algorithm is the Dijsktra path search algorithm, which is applied to a Voronoi mesh. MOLE is also powerful in the exploration of large molecular channels, complex networks of channels in a single structure or structures from molecular dynamics trajectories (AMBER ascii traj and parm7 are supported).

PMFLib

PMFLib

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.

SiteBinder

SiteBinder

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.