Search Results - "Plewczynski, D"

Detecting reliable non interacting proteins (NIPs) significantly enhancing the computational prediction of protein-protein interactions using machine learning methods by Srivastava, A, Mazzocco, G, Kel, A, Wyrwicz, L S, Plewczynski, D

“…Protein-protein interactions (PPIs) play a vital role in most biological processes. Hence their comprehension can promote a better understanding of the…”
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Oncogenes expand during evolution to withstand somatic amplification by Wang, X., Li, X., Zhang, L., Wong, S.H., Wang, M.H.T., Tse, G., Dai, R.Z.W., Nakatsu, G., Coker, O.O., Chen, Z., Ko, H., Chan, J.Y.K., Liu, T., Cheng, C.H.K., Cheng, A.S.L., To, K.F., Plewczynski, D., Sung, J.J.Y., Yu, J., Gin, T., Chan, M.T.V., Wu, W.K.K.

“…Cancer-related genes are under intense evolutionary pressure. We conjectured that gene size is an important determinant of amplification propensity for…”
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AutoMotif server: prediction of single residue post-translational modifications in proteins by Plewczynski, Dariusz, Tkacz, Adrian, Wyrwicz, Lucjan Stanislaw, Rychlewski, Leszek

“…The AutoMotif Server allows for identification of post-translational modification (PTM) sites in proteins based only on local sequence information. The local…”
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Protein-protein interaction and pathway databases, a graphical review by Klingström, Tomas, Plewczynski, Dariusz

“…The amount of information regarding protein-protein interactions (PPI) at a proteomic scale is constantly increasing. This is paralleled with an increase of…”
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Abstract P3-09-07: The role of MLK4 amplification in progression of triple negative breast cancer by Prelowska, MK, Mehlich, D, Lazniewski, M, Kaminska, K, Gorczynski, AS, Korwat, A, Sokolowska, O, Golab, J, Biernat, W, Plewczynski, D, Brognard, J, Nowis, D, Marusiak, AA

“…Mixed Lineage Kinase 4 (MLK4) is a serine/threonine kinase that plays a role in a variety of cellular processes, including migration, apoptosis and…”
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SVMeFC: SVM Ensemble Fuzzy Clustering for Satellite Image Segmentation by Saha, I., Maulik, U., Bandyopadhyay, S., Plewczynski, D.

“…The problem of unsupervised image segmentation of a satellite image in a number of homogeneous regions can be viewed as the task of clustering the pixels in…”
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TVscreen: Trend Vector Virtual SCREENing of Large Commercial Compounds Collections by Plewczynski, D.

“…We present here the trend vector based method for identification of inhibitors for a given protein target. Therefore our approach reduces the number of…”
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3D-Hit: fast structural comparison of proteins on multicore architectures by Bieniasz-Krzywiec, Ł., Cytowski, M., Rychlewski, L., Plewczynski, D.

“…3D-Hit is a well established method for rapid detection of structural similarities between proteins, which is widely used in various bioinformatics web servers…”
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Approach to equilibrium of particles diffusing on curved surfaces by Plewczyński, D., Hołyst, R.

“…We present a simple numerical analysis of the diffusion on a curved surface given by the equation φ( r )=0 in a finite domain D ⊂ R 3 . The first non-vanishing…”
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Prediction of signal peptides in protein sequences by neural networks by Plewczynski, Dariusz, Slabinski, Lukasz, Ginalski, Krzysztof, Rychlewski, Leszek

“…We present here a neural network-based method for detection of signal peptides (abbreviation used: SP) in proteins. The method is trained on sequences of known…”
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Landau theory of social clustering by Plewczyński, Dariusz

“…We discuss the Landau theory for a nonlinear equation that can describe social changes, such as an influence of the social environment on individual. The…”
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3D-Fun: predicting enzyme function from structure by von Grotthuss, Marcin, Plewczynski, Dariusz, Vriend, Gert, Rychlewski, Leszek

“…The 'omics' revolution is causing a flurry of data that all needs to be annotated for it to become useful. Sequences of proteins of unknown function can be…”
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PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics by von Grotthuss, Marcin, Plewczynski, Dariusz, Ginalski, Krzysztof, Rychlewski, Leszek, Shakhnovich, Eugene I

“…The number of protein structures from structural genomics centers dramatically increases in the Protein Data Bank (PDB). Many of these structures are…”
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A support vector machine approach to the identification of phosphorylation sites by Plewczyński, Dariusz, Tkacz, Adrian, Godzik, Adam, Rychlewski, Leszek

“…We describe a bioinformatics tool that can be used to predict the position of phosphorylation sites in proteins based only on sequence information. The method…”
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Molecular modeling of phosphorylation sites in proteins using a database of local structure segments by Plewczynski, Dariusz, Jaroszewski, Lukasz, Godzik, Adam, Kloczkowski, Andrzej, Rychlewski, Leszek

“…A new bioinformatics tool for molecular modeling of the local structure around phosphorylation sites in proteins has been developed. Our method is based on a…”
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Integrated web service for improving alignment quality based on segments comparison by Plewczynski, Dariusz, Rychlewski, Leszek, Ye, Yuzhen, Jaroszewski, Lukasz, Godzik, Adam

“…Defining blocks forming the global protein structure on the basis of local structural regularity is a very fruitful idea, extensively used in description, and…”
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Comparison of proteins based on segments structural similarity by Plewczynski, Dariusz, Pas, Jakub, Von Grotthuss, Marcin, Rychlewski, Leszek

“…We present here a simple method for fast and accurate comparison of proteins using their structures. The algorithm is based on structural alignment of segments…”
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Support-vector-machine classification of linear functional motifs in proteins by Plewczynski, Dariusz, Tkacz, Adrian, Wyrwicz, Lucjan Stanisław, Godzik, Adam, Kloczkowski, Andrzej, Rychlewski, Leszek

“…Our algorithm predicts short linear functional motifs in proteins using only sequence information. Statistical models for short linear functional motifs in…”
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Diffusion on curved, periodic surfaces by Hołyst, R, Plewczyński, D, Aksimentiev, A, Burdzy, K

“…We present a simulation algorithm for a diffusion on a curved surface given by the equation phi(r)=0. The algorithm is tested against analytical results known…”
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Influence of colored noise on chaotic systems by Redaelli, Stefano, Plewczyński, Dariusz, Macek, Wiesław M

“…We focus on classical chaotic systems corrupted by white and colored noise. We study the dependence of the correlation dimension and the Kolmogorov entropy on…”
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