Answering the issue of 'Cybernetics Modelling of Biological Systems' covers a large spectrum of dimensions, starting from the molecular level up to the population level. If one remains at the scale of molecules, historically, the first method is the so-called comparative modelling, aiming at producing the model of a protein from the structure of a homologous sequence. Nowadays, several services over the web are able to produce in a reasonable computer time a model of most of the query sequences, provided one sample of their architecture is already deposited in one of the structural databases. In the meantime, large improvements in the algorithms designed to decipher distant relations among sequences sharing one common ancestor have increased the quality of the annotations in the sequence databases, in particular because of their ability to transfer information from a related protein. Then the prediction of complexes came in the game, either concerning proteinprotein interactions, or protein ligand, and more recently protein peptide docking. Another aspect concerns dynamics of proteins, with the increasing power of computers or the parallel use of huge numbers of CPUs, and the improvement of the algorithms. Although it is not a routine task, the folding of some small proteins has been achieved on dedicated hardware for trajectories of several milliseconds. Simulations can give access to the intermediate states a protein goes through during its folding process. Besides, analysis of dynamic processes allowed to give insights into thermodynamics, and more and more accurate free energy predictions are available, giving some view on the effects of a point mutation on the structure, and hence, on the function. Department of Medical Biotechnology, Jagiellonian University, Poland A protein folding is a biological process aimed at creation of a fully functional protein starting from a linear chain of amino acids. Being able to predict a correct result of the mentioned process using in silico methods is very crucial for drug design, especially in an aspect of personal therapy. This abstract describes a concept, an implementation and exemplary results of the protein folding process simulator developed for PLGrid NG project. The tool uses two-step model which is composed of an Early and a Late stages [1]. A preparation of an initially formed 3D conformation with secondary structures drafts for a given amino acid sequence is an objective of the Early Stage. An output of this stage is optimized in the next step using an internal (electrostatic, torsional potential and van der Waals) and an external (influence of water surrounding) force field. Currently, the software is prepared for a so-called '3D Gauss accordant' protein -it means that spatial positions of protein residues satisfy a 3D Gauss hydrophobicity model. The simulations for several of such structures were executed and some of the results revealed quite high similarity with the native structure (e.g. TM-score 5.3 and RMSD 3.0). Results of the simulations are promisin...