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< Back Structure and Function Prediction Structure Prediction Variation of Geometrical and Physicochemical Properties in Protein Binding Pockets and their Ligands Abdullah Kahraman, Richard J. Morris, Roman A. Laskowski, Janet M. Thornton EBI, United Kingdom The variation of the ligand and binding pocket shape together with the variation of the hydrophobicity, van-der-Waals and electrostatic potential on the ligand surface were analysed in different proteins. A correlation between ligand and binding site could be detected only for shape and hydrophobicity indicating their importance for molecular recognition. Download PDF of full abstract. Structure Prediction Predicting local structure using sequence information Huzefa Rangwala, George Karypis University of MInnesota, Twin Cities, United States Motivated by the alignment requirements of comparative modeling approaches and the operational characteristics of protein structure alignment algorithms, we estimate the RMSD value between a pair of protein fragments by considering only sequence-derived information. For protein pairs with low sequence similarity less then (12%), these new structural features lead to improved alignments. Download PDF of full abstract. Structure Prediction Homology Modeling of a Voltage-gated Potassium channel (Human Kv7.1) Alexandr Goncearenco, Yasmin Karimi-Nejad, Konrad Koehler Cologne University Bioinformatics Center, Germany Homology models of Long QT Syndrome related KCNQ1 potassium channel were built and assessed using experimental data. Proof-of-principle for their use in a virtual screening protocol is given. It is suggested that conformational changes could be induced to improve blockade predictions. A PyMOL plugin is proposed. Download PDF of full abstract. Structure Prediction Modelling Co-translational Protein Folding Rhodri Saunders, Charlotte Deane University of Oxford, United Kingdom Under co-translational folding a protein folds sequentially from the N-terminus as it is translated. We use simplified models to identify the characterisitics of co-translationally folded structures. Significant differences are observed between co-translatinal folders and all others. We are now investigating these characteristics in real protein structures. Download PDF of full abstract. Structure Prediction Membrane Protein Structure Prediction: Influence of Distance Constraints on the Efficiency of the Conformational Search with Monte Carlo Simulation Claire Gervais, Zhong Chen, Ying Xu University of Georgia, United States We present our approach for ab initio prediction of alpha-helix transmembrane structures.Monte Carlo simulations are carried out using the Wang-Landau algorithm. We show how to include experimental data (e.g. in form of distance constraints) in the conformational search procedure in order to increase the overall efficiency of the algorithm. Download PDF of full abstract. |