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Frontmatter

Frontmatter BIO-ALGORITHMS AND MED-SYSTEMS EDITOR-IN-CHIEF Irena Roterman-Konieczna, Krakow HONORARY ADVISOR Ryszard Tadeusiewicz, Krakow SCIENTIFIC COMMITTEE Piotr Augustyniak, Krakow Adam S.Z. Belloum, Amsterdam Michal Brylinski, Baton Rouge, LA Marian Bubak, Krakow Jacques Chomilier, Paris Marc Ebner, Tübingen Dragan Gamberger, Zagreb Inga Hege, Munich Sören Huwendiek, Heidelberg Wiktor Jurkowski, Luxembourg Kalina Kawecka-Jaszcz, Krakow Leszek Konieczny, Krakow Valeria Krzhizhanovskaya, Amsterdam Silvia Delgado Olabarriaga, Amsterdam Gabriele Pierantoni, Dublin Fabio Polticelli, Rome Mikhail Posypkin, Moscow Thomas Röblitz, Göttingen Reinhard Schneider, Luxembourg Pawel Spolnik, Krakow Katarzyna Sta por, Gliwice Andrzej Walczak, Warsaw Nabil Zary, Stockholm ABSTRACTED/INDEXED IN BazTech; Celdes; CNKI Scholar (China National Knowledge Infrastucture); CNPIEC; EBSCO Discovery Service; Google Scholar; Index Copernicus; J-Gate; Naviga (Softweco); Primo Central (ExLibris); PubsHub; Summon (Serials Solutions/ProQuest); TDOne (TDNet); WorldCat (OCLC) All information regarding notes for contributors, subscriptions, Open access, back volumes and orders is available online at www.degruyter.de/bams The publisher, together with the authors and editors, has taken great pains to ensure that all information presented in this work (programs, applications, amounts, dosages, etc.) reflects the standard of knowledge at the time of publication. Despite careful manuscript preparation and proof correction, errors can nevertheless occur. Authors, editors and publisher disclaim all responsibility for any errors or omissions or liability for the results obtained from use of the information, or parts thereof, contained in this work. The citation of registered names, trade names, trademarks, etc. in this work does not imply, even in the absence of a specific statement, that such names are exempt from laws and regulations protecting trademarks etc. and therefore free for general use. ISSN 1895-9091 · e-ISSN 1896-530X RESPONSIBLE EDITOR Irena Roterman-Konieczna, Department of Bioinformatics and Telemedicine, Jagiellonian University ­ Medical College, Lazarza 16, 31-530 Krakow, Poland, Tel.: +48 (0)12 6199693, Fax: +48 (0)12 6199693, Email: iroterman@cm-uj.krakow.pl TECHNICAL EDITORS Piotr Walecki, Zdzislaw Wisniowski, Anna Zaremba-Smietanska, Jagiellonian University Medical College, Department of Bioinformatics and Telemedicine, Sw. Lazarza 16, 31-530 Krakow, Poland, Tel.: +48 (0)12 6199693, Fax: +48 (0)12 6199693, Email: bams@cm-uj.krakow.pl JOURNAL MANAGER Heike Jahnke, De Gruyter, Genthiner Straße 13, 10785 Berlin, Germany, Tel.: +49 (0)30 260 05-220, Fax: +49 (0)30 260 05-325, Email: heike.jahnke@degruyter.com RESPONSIBLE FOR ADVERTISEMENTS Claudia Neumann, De Gruyter, Genthiner Straße 13, 10785 Berlin, Germany, Tel.: +49 (0)30 260 05-226, Fax: +49 (0)30 260 05-322, Email: anzeigen@degruyter.com © 2014 Walter de Gruyter GmbH, Berlin/Munich/Boston TYPESETTING Compuscript Ltd., Shannon, Ireland PRINTING Franz X. Stückle Druck und Verlag e. K, Ettenheim Printed in Germany Bio-Algorithms and Med-Systems 2014 | Volume 10 | Issue 4 Contents Special issue: The early steps of the folding of globular proteins Guest Editor: Jacques Chomilier Editorial Jacques Chomilier Some insights into the transition state ensemble of the folding of globular proteins 167 Martin Mann and Rolf Backofen Exact methods for lattice protein models Reviews Tomer Orevi, Gil Rahamim, Sivan Shemesh, Eldad Ben Ishay, Dan Amir and Elisha Haas Fast closure of long loops at the initiation of the folding transition of globular proteins studied by time-resolved FRET-based methods 169 Jaume Bonet, Andras Fiser, Baldo Oliva and Narcis Fernandez-Fuentes Smotifs as structural local descriptors of supersecondary elements: classification, completeness and applications 195 Ruben Acuña, Zoé Lacroix, Nikolaos Papandreou and Jacques Chomilier Protein intrachain contact prediction with most interacting residues (MIR) 227 Stuart Tetchner, Tomasz Kosciolek and David T. Jones Opportunities and limitations in applying coevolutionderived contacts to protein structure prediction 243 http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Bio-Algorithms and Med-Systems de Gruyter

Frontmatter

Bio-Algorithms and Med-Systems , Volume 10 (4) – Dec 19, 2014
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de Gruyter
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1895-9091
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1896-530X
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Abstract

BIO-ALGORITHMS AND MED-SYSTEMS EDITOR-IN-CHIEF Irena Roterman-Konieczna, Krakow HONORARY ADVISOR Ryszard Tadeusiewicz, Krakow SCIENTIFIC COMMITTEE Piotr Augustyniak, Krakow Adam S.Z. Belloum, Amsterdam Michal Brylinski, Baton Rouge, LA Marian Bubak, Krakow Jacques Chomilier, Paris Marc Ebner, Tübingen Dragan Gamberger, Zagreb Inga Hege, Munich Sören Huwendiek, Heidelberg Wiktor Jurkowski, Luxembourg Kalina Kawecka-Jaszcz, Krakow Leszek Konieczny, Krakow Valeria Krzhizhanovskaya, Amsterdam Silvia Delgado Olabarriaga, Amsterdam Gabriele Pierantoni, Dublin Fabio Polticelli, Rome Mikhail Posypkin, Moscow Thomas Röblitz, Göttingen Reinhard Schneider, Luxembourg Pawel Spolnik, Krakow Katarzyna Sta por, Gliwice Andrzej Walczak, Warsaw Nabil Zary, Stockholm ABSTRACTED/INDEXED IN BazTech; Celdes; CNKI Scholar (China National Knowledge Infrastucture); CNPIEC; EBSCO Discovery Service; Google Scholar; Index Copernicus; J-Gate; Naviga (Softweco); Primo Central (ExLibris); PubsHub; Summon (Serials Solutions/ProQuest); TDOne (TDNet); WorldCat (OCLC) All information regarding notes for contributors, subscriptions, Open access, back volumes and orders is available online at www.degruyter.de/bams The publisher, together with the authors and editors, has taken great pains to ensure that all information presented in this work (programs, applications, amounts, dosages, etc.) reflects the standard of knowledge at the time of publication. Despite careful manuscript preparation and proof correction, errors can nevertheless occur. Authors, editors and publisher disclaim all responsibility for any errors or omissions or liability for the results obtained from use of the information, or parts thereof, contained in this work. The citation of registered names, trade names, trademarks, etc. in this work does not imply, even in the absence of a specific statement, that such names are exempt from laws and regulations protecting trademarks etc. and therefore free for general use. ISSN 1895-9091 · e-ISSN 1896-530X RESPONSIBLE EDITOR Irena Roterman-Konieczna, Department of Bioinformatics and Telemedicine, Jagiellonian University ­ Medical College, Lazarza 16, 31-530 Krakow, Poland, Tel.: +48 (0)12 6199693, Fax: +48 (0)12 6199693, Email: iroterman@cm-uj.krakow.pl TECHNICAL EDITORS Piotr Walecki, Zdzislaw Wisniowski, Anna Zaremba-Smietanska, Jagiellonian University Medical College, Department of Bioinformatics and Telemedicine, Sw. Lazarza 16, 31-530 Krakow, Poland, Tel.: +48 (0)12 6199693, Fax: +48 (0)12 6199693, Email: bams@cm-uj.krakow.pl JOURNAL MANAGER Heike Jahnke, De Gruyter, Genthiner Straße 13, 10785 Berlin, Germany, Tel.: +49 (0)30 260 05-220, Fax: +49 (0)30 260 05-325, Email: heike.jahnke@degruyter.com RESPONSIBLE FOR ADVERTISEMENTS Claudia Neumann, De Gruyter, Genthiner Straße 13, 10785 Berlin, Germany, Tel.: +49 (0)30 260 05-226, Fax: +49 (0)30 260 05-322, Email: anzeigen@degruyter.com © 2014 Walter de Gruyter GmbH, Berlin/Munich/Boston TYPESETTING Compuscript Ltd., Shannon, Ireland PRINTING Franz X. Stückle Druck und Verlag e. K, Ettenheim Printed in Germany Bio-Algorithms and Med-Systems 2014 | Volume 10 | Issue 4 Contents Special issue: The early steps of the folding of globular proteins Guest Editor: Jacques Chomilier Editorial Jacques Chomilier Some insights into the transition state ensemble of the folding of globular proteins 167 Martin Mann and Rolf Backofen Exact methods for lattice protein models Reviews Tomer Orevi, Gil Rahamim, Sivan Shemesh, Eldad Ben Ishay, Dan Amir and Elisha Haas Fast closure of long loops at the initiation of the folding transition of globular proteins studied by time-resolved FRET-based methods 169 Jaume Bonet, Andras Fiser, Baldo Oliva and Narcis Fernandez-Fuentes Smotifs as structural local descriptors of supersecondary elements: classification, completeness and applications 195 Ruben Acuña, Zoé Lacroix, Nikolaos Papandreou and Jacques Chomilier Protein intrachain contact prediction with most interacting residues (MIR) 227 Stuart Tetchner, Tomasz Kosciolek and David T. Jones Opportunities and limitations in applying coevolutionderived contacts to protein structure prediction 243

Journal

Bio-Algorithms and Med-Systems – de Gruyter

Published: Dec 19, 2014

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