University of Warsaw

About: University of Warsaw is a education organization based out in Warsaw, Poland. It is known for research contribution in the topics: Population & Large Hadron Collider. The organization has 20832 authors who have published 56617 publications receiving 1185084 citations. The organization is also known as: Uniwersytet Warszawski & Warsaw University.

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site

Abstract: Protein-peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein-peptide interactions using a highly efficient protocol for the flexible docking of peptides to proteins. While other docking algorithms require pre-defined localization of the binding site, CABS-dock doesn't require such knowledge. Given a protein receptor structure and a peptide sequence (and starting from random conformations and positions of the peptide), CABS-dock performs simulation search for the binding site allowing for full flexibility of the peptide and small fluctuations of the receptor backbone. This protocol was extensively tested over the largest dataset of non-redundant protein-peptide interactions available to date (including bound and unbound docking cases). For over 80% of bound and unbound data set cases, we obtained models with high or medium accuracy (sufficient for practical applications). Additionally, as optional features, CABS-dock can exclude user-selected binding modes from docking search or to increase the level of flexibility for chosen receptor fragments. CABS-dock is freely available as a web server at this http URL

BASECOL2012: A collisional database repository and web service within the Virtual Atomic and Molecular Data Centre (VAMDC)

Abstract: The BASECOL2012 database is a repository of collisional data and a web service within the Virtual Atomic and Molecular Data Centre (VAMDC, http://www.vamdc.eu). It contains rate coefficients for the collisional excitation of rotational, ro-vibrational, vibrational, fine, and hyperfine levels of molecules by atoms, molecules, and electrons, as well as fine-structure excitation of some atoms that are relevant to interstellar and circumstellar astrophysical applications. Submissions of new published collisional rate coefficients sets are welcome, and they will be critically evaluated before inclusion in the database. In addition, BASECOL2012 provides spectroscopic data queried dynamically from various spectroscopic databases using the VAMDC technology. These spectroscopic data are conveniently matched to the in-house collisional excitation rate coefficients using the SPECTCOL sofware package (http:// vamdc.eu/software), and the combined sets of data can be downloaded from the BASECOL2012 website. As a partner of the VAMDC, BASECOL2012 is accessible from the general VAMDC portal (http://portal.vamdc.eu) and from user tools such as SPECTCOL.

A $c^k n$ 5-Approximation Algorithm for Treewidth

Abstract: We give an algorithm that for an input $n$-vertex graph $G$ and integer $k>0$, in time $2^{O(k)} n$, either outputs that the treewidth of $G$ is larger than $k$, or gives a tree decomposition of $G$ of width at most $5k+4$. This is the first algorithm providing a constant factor approximation for treewidth which runs in time single exponential in $k$ and linear in $n$. Treewidth-based computations are subroutines of numerous algorithms. Our algorithm can be used to speed up many such algorithms to work in time which is single exponential in the treewidth and linear in the input size.

Measurement of the differential cross section for top quark pair production in pp collisions at √s=8 TeV

Abstract: The normalized differential cross section for top quark pair (tt) production is measured in pp collisions at a centre-of-mass energy of 8TeV at the CERN LHC using the CMS detector in data corresponding to an integrated luminosity of 19.7fb^(−1). The measurements are performed in the lepton+jets (e/μ +jets) and in the dilepton (e^+e^−, μ^+μ^−, and e^±μ^∓) decay channels. The tt cross section is measured as a function of the kinematic properties of the charged leptons, the jets associated to b quarks, the top quarks, and the tt system. The data are compared with several predictions from perturbative quantum chromodynamic up to approximate next-to-next-to-leading-order precision. No significant deviations are observed relative to the standard model predictions.