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Determining critical amino acid contacts for knotted protein folding

Dąbrowski-Tumański P., Niewieczerzał S., Sułkowska J. I.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

2014

Vol. 18, No 3

265--279

Proteins with a non-trivial topological structure are currently well recognized, while a knotted protein chain represents a new motif in protein three dimensional folds. Recent comprehensive analysis of the Protein Data Base shows that knotted proteins represent 1.5% of known protein structures. Determination of a free energy landscape of knotted proteins, and its understanding provides a serious challenge for both experimentalists and theoreticians. Moreover the role of a knot for biological activity of protein still remains elusive. In this work we study the smallest knotted proteins ( PDB code 2efv) to understand/investigate their free energy landscape, by means of extensive molecular dynamics simulations. We explore the dependence of the thermodynamics, kinetics and protein folding pathways on the native-likes contact maps and on the length of the chain. We analyze two sets of native-like contacts , which differ by a number of long range interactions, and we consider the 2efv protein with two different lengths of its C-terminus end. We identify the subset of native contacts sufficient to explore the entire free energy landscape. Then, we analyze the influence of the remaining set of native contacts – we show that the set of additional contacts may enhance folding kinetics, and that it has an influence on folding pathways.

Nitano - novel inter/intramolecular colocation calculator

Kuśka J., Leluk J., Lesyng B.

Bio-Algorithms and Med-Systems

2010

Vol. 6, no. 12

91--97

Nitano is a stand-alone Windows application. The main purpose of this software is to calculate the intra- or intermolecular residue colocations. A PDB file is used as input file. The application is to detect and analyse the intramolecular contacts as well as the contacts between residues from two separate chains/molecules (see Fig. 2). Nitano can be used for study the proteins and nucleic acids. The output files contain names, numbers and distances between the atoms that reveal collocation. The application gives two types of maps that show the structure on a two-dimensional image. Nitano allows to perform basic statistical analysis of obtained results. This application is a useful tool supporting the work of drug designers in creating more specific ligands. The application is freely available for educational and academic purposes at: http://www.bioware.republika.pl. Nitano is a user friendly application and does not require any advanced course to be applied for any kind of analysis.