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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.

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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.

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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.

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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.

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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.

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