Anton A Polyansky1, Anton O Chugunov, Pavel E Volynsky, Nikolay A Krylov, Dmitry E Nolde, Roman G Efremov. 1. M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia, Max F. Perutz Laboratories, Department of Structural and Computational Biology, University of Vienna, Campus Vienna Biocenter 5, Vienna AT-1030, Austria and Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region 141700, Russia.
Abstract
SUMMARY: Here we present PREDDIMER, a web tool for prediction of dimer structure of transmembrane (TM) helices. PREDDIMER allows (i) reconstruction of a number of dimer structures for given sequence(s) of TM protein fragments, (ii) ranking and filtering of predicted structures according to respective values of a scoring function, (iii) visualization of predicted 3D dimer structures and (iv) visualization of surface hydrophobicity of TM helices and their contacting (interface) regions represented as 2D maps. RESULTS: We implemented online the original PREDDIMER algorithm and benchmarked the server on 11 TM sequences, whose 3D dimer conformations were obtained previously by nuclear magnetic resonance spectroscopy. In the most of tested cases backbone root-mean-square deviations of closest predicted conformations from the experimental reference are below 3 Å. A randomization test displays good anticorrelation (-0.82) between values of the scoring function and statistical significance of the prediction 'by chance'. Going beyond a single dimer conformation, our web tool predicts an ensemble of possible conformations, which may be useful for explanation of a functioning of bitopic membrane proteins, e.g. receptor tyrosine kinases. AVAILABILITY AND IMPLEMENTATION: PREDDIMER can be accessed for free on the web at http://model.nmr.ru/preddimer/ CONTACT: newant@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: Here we present PREDDIMER, a web tool for prediction of dimer structure of transmembrane (TM) helices. PREDDIMER allows (i) reconstruction of a number of dimer structures for given sequence(s) of TM protein fragments, (ii) ranking and filtering of predicted structures according to respective values of a scoring function, (iii) visualization of predicted 3D dimer structures and (iv) visualization of surface hydrophobicity of TM helices and their contacting (interface) regions represented as 2D maps. RESULTS: We implemented online the original PREDDIMER algorithm and benchmarked the server on 11 TM sequences, whose 3D dimer conformations were obtained previously by nuclear magnetic resonance spectroscopy. In the most of tested cases backbone root-mean-square deviations of closest predicted conformations from the experimental reference are below 3 Å. A randomization test displays good anticorrelation (-0.82) between values of the scoring function and statistical significance of the prediction 'by chance'. Going beyond a single dimer conformation, our web tool predicts an ensemble of possible conformations, which may be useful for explanation of a functioning of bitopic membrane proteins, e.g. receptor tyrosine kinases. AVAILABILITY AND IMPLEMENTATION: PREDDIMER can be accessed for free on the web at http://model.nmr.ru/preddimer/ CONTACT: newant@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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