Ceslovas Venclovas

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UNLABELLED We present Voroprot, an interactive cross-platform software tool that provides a unique set of capabilities for exploring geometric features of protein structure. Voroprot allows the construction and visualization of the Apollonius diagram (also known as the additively weighted Voronoi diagram), the Apollonius graph, protein alpha shapes,(More)
CASP has now completed a decade of monitoring the state of the art in protein structure prediction. The quality of structure models produced in the latest experiment, CASP6, has been compared with that in earlier CASPs. Significant although modest progress has again been made in the fold recognition regime, and cumulatively, progress in this area is(More)
The quality of structure models produced in the CASP5 experiment has been compared with that in earlier CASPs. The most significant progress is in the fold recognition regime, where the development of meta-servers has allowed more accurate consensus models to be generated. In contrast to this, there is little evidence of progress in producing more accurate(More)
The repair of damaged DNA is coupled to the completion of DNA replication by several cell cycle checkpoint proteins, including, for example, in fission yeast Rad1(Sp), Hus1(Sp), Rad9(Sp) and Rad17(Sp). We have found that these four proteins are conserved with protein sequences throughout eukaryotic evolution. Using computational techniques, including fold(More)
Models for 20 comparative modeling targets were submitted for the fifth round of the "blind" test of protein structure prediction methods (CASP5; http://predictioncenter.llnl.gov/casp5). The modeling approach used in CASP5 was similar to that used 2 years ago in CASP4 (Venclovas, Proteins 2001; Suppl 5:47-54). The main features of this approach include use(More)
The MYH (MutY glycosylase homologue) increases replication fidelity by removing adenines or 2-hydroxyadenine misincorporated opposite GO (7,8-dihydro-8-oxo-guanine). The 9-1-1 complex (Rad9, Rad1 and Hus1 heterotrimer complex) has been suggested as a DNA damage sensor. Here, we report that hMYH (human MYH) interacts with hHus1 (human Hus1) and hRad1 (human(More)
SUMMARY Detection of distant homology is a widely used computational approach for studying protein evolution, structure and function. Here, we report a homology search web server based on sequence profile-profile comparison. The user may perform searches in one of several regularly updated profile databases using either a single sequence or a multiple(More)
MOTIVATION Herpesviruses are large DNA viruses causing a variety of diseases in humans and animals. To develop effective treatment, it is important to understand the mechanisms of their replication. One of the components of the herpesviral DNA replication system is a helicase-primase complex, consisting of UL5 (helicase), UL52 (primase) and UL8. UL8 is an(More)
The Voronoi diagram of balls, corresponding to atoms of van der Waals radii, is particularly well-suited for the analysis of three-dimensional structures of biological macromolecules. However, due to the shortage of practical algorithms and the corresponding software, simpler approaches are often used instead. Here, we present a simple and robust algorithm(More)