caa a22 4500 475845129 CHVBK 20180406123912.0 cr unu---uuuuu 170329e20001201xx s 000 0 eng 10.1007/PL00000677 doi (NATIONALLICENCE)springer-10.1007/PL00000677 Protein surface similarities: a survey of methods to describe and compare protein surfaces [Elektronische Daten] [A. Via, F. Ferrè, B. Brannetti, M. Helmer-Citterich*] Abstract.: Many methods have been developed to analyse protein sequences and structures, although less work has been undertaken describing and comparing protein surfaces. Evolution can lead sequences to diverge or structures to change topology; nevertheless, surface determinants that are essential to protein function itself may be mantained. Moreover, different molecules could converge to similar functions by gaining specific surface determinants. In such cases, sequence or structure comparisons are likely to be inadequate in describing or identifying protein functions and evolutionary relationships among proteins. Surface analysis can identify function determinants that are independent of sequence or secondary structure and can therefore be a powerful tool to highlight cases of possible convergent or divergent evolution. This kind of approach can be useful for a better understanding of protein molecular and biochemical mechanisms of catalysis or interaction with a ligand, which are usually surface dependent. Protein surface comparison, when compared to sequence or structure comparison methods, is a hard computational challenge and evaluated methods allowing the comparison of protein surfaces are difficult to find. In this review, we will survey the current knowledge about protein surface similarity and the techniques to detect it. Birkhäuser Verlag Basel,, 2000 Key words. Protein surface nationallicence surface comparison nationallicence patterns nationallicence molecular evolution nationallicence Via A. Centro di Bioinformatica Molecolare, Department of Biology, University of Rome ‘Tor Vergata', via della Ricerca Scientifica, 00133 Rome (Italy), Fax +39 06 2023500, e-mail: citterich@uniroma2.it, IT aut Ferrè F. Centro di Bioinformatica Molecolare, Department of Biology, University of Rome ‘Tor Vergata', via della Ricerca Scientifica, 00133 Rome (Italy), Fax +39 06 2023500, e-mail: citterich@uniroma2.it, IT aut Brannetti B. Centro di Bioinformatica Molecolare, Department of Biology, University of Rome ‘Tor Vergata', via della Ricerca Scientifica, 00133 Rome (Italy), Fax +39 06 2023500, e-mail: citterich@uniroma2.it, IT aut Helmer-Citterich* M. Centro di Bioinformatica Molecolare, Department of Biology, University of Rome ‘Tor Vergata', via della Ricerca Scientifica, 00133 Rome (Italy), Fax +39 06 2023500, e-mail: citterich@uniroma2.it, IT aut https://doi.org/10.1007/PL00000677 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/PL00000677 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Via A. Centro di Bioinformatica Molecolare, Department of Biology, University of Rome ‘Tor Vergata', via della Ricerca Scientifica, 00133 Rome (Italy), Fax +39 06 2023500, e-mail: citterich@uniroma2.it, IT aut NATIONALLICENCE 700 1- Ferrè F. Centro di Bioinformatica Molecolare, Department of Biology, University of Rome ‘Tor Vergata', via della Ricerca Scientifica, 00133 Rome (Italy), Fax +39 06 2023500, e-mail: citterich@uniroma2.it, IT aut NATIONALLICENCE 700 1- Brannetti B. Centro di Bioinformatica Molecolare, Department of Biology, University of Rome ‘Tor Vergata', via della Ricerca Scientifica, 00133 Rome (Italy), Fax +39 06 2023500, e-mail: citterich@uniroma2.it, IT aut NATIONALLICENCE 700 1- Helmer-Citterich* M. Centro di Bioinformatica Molecolare, Department of Biology, University of Rome ‘Tor Vergata', via della Ricerca Scientifica, 00133 Rome (Italy), Fax +39 06 2023500, e-mail: citterich@uniroma2.it, IT aut Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer