Biomedical subjects

Frantisek Pavelcik

Publications and source records attributed to Frantisek Pavelcik.

3 recordsLinked to original sources

PubMed2004

Accurate automatic protein models.

A method for automatic building of protein structures has been developed. The method is based on the concept of flexible structure units. A structure unit is a fragment (group) of about ten atoms that is positioned in the electron density by a phased rotation and translation function. The positions, orientations and internal torsion angles of all structure units are refined by a phased flexible refinement. Individual structure units are connected into polyalanine chains. The sequence is aligned by combined marker and rotamer methods. The side chains are built either by the marker method and a full conformational search or by the rotamer method. Side chains are independent structure units. The structure unit represents a generalized atom and the group model can be refined by the least-squares method. The protein model is built with an accuracy of about 0.2 A at resolutions of 1.2-1.9 A. Partial results can be obtained at resolutions of between 2.0 and 2.3 A.

Algorithms↗

PubMed2003

Automatic model building based on flexible fragment formalism. The case of high-resolution protein structures.

A concept of flexible fragments has been developed for automatic building of crystal structures. Six monopeptides were designed as search fragments in a phased rotation and translation function for protein building. Electron density in crystal and in molecular fragments is expanded in spherical harmonics and normalized spherical Bessel functions. A fast rotation function, which is calculated at each grid point of the asymmetric unit, is used to find the fragment orientation. Position, orientation and internal torsion angles are refined. An algorithm for chain building is simplified using generalized atoms and virtual bonds. The structure is built from molecular structure units rather than from individual atoms. A polyalanine model is built with a high accuracy at resolutions 1.2-2.1 A.

Models, Molecular↗

PubMed2002

Methodology and applications of automatic electron-density map interpretation by six-dimensional rotational and translational search for molecular fragments.

The electron density for a search fragment and for the crystal is expanded in the space of spherical harmonics Bessel functions. The fast rotation function is evaluated for each grid point to test if the fragment can be orientated there. For the best scoring points, the six-dimensional coordinates of the fragment are refined by the second-derivative block-diagonal procedure. The method is able to locate fragments precisely over a wide range of resolutions for structure types from small organic molecules to proteins.

Bacterial Proteins↗