Literature DB >> 22639196

MaxOcc: a web portal for maximum occurrence analysis.

Ivano Bertini1, Lucio Ferella, Claudio Luchinat, Giacomo Parigi, Maxim V Petoukhov, Enrico Ravera, Antonio Rosato, Dmitri I Svergun.   

Abstract

The MaxOcc web portal is presented for the characterization of the conformational heterogeneity of two-domain proteins, through the calculation of the Maximum Occurrence that each protein conformation can have in agreement with experimental data. Whatever the real ensemble of conformations sampled by a protein, the weight of any conformation cannot exceed the calculated corresponding Maximum Occurrence value. The present portal allows users to compute these values using any combination of restraints like pseudocontact shifts, paramagnetism-based residual dipolar couplings, paramagnetic relaxation enhancements and small angle X-ray scattering profiles, given the 3D structure of the two domains as input. MaxOcc is embedded within the NMR grid services of the WeNMR project and is available via the WeNMR gateway at http://py-enmr.cerm.unifi.it/access/index/maxocc . It can be used freely upon registration to the grid with a digital certificate.

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Year:  2012        PMID： 22639196     DOI： 10.1007/s10858-012-9638-1

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN： 0925-2738            Impact factor:   2.835


  32 in total

1.  Experimentally exploring the conformational space sampled by domain reorientation in calmodulin.

Authors:  Ivano Bertini; Cristina Del Bianco; Ioannis Gelis; Nikolaus Katsaros; Claudio Luchinat; Giacomo Parigi; Massimiliano Peana; Alessandro Provenzani; Maria Antonietta Zoroddu
Journal:  Proc Natl Acad Sci U S A       Date:  2004-04-20       Impact factor: 11.205

2.  Conformational space of flexible biological macromolecules from average data.

Authors:  Ivano Bertini; Andrea Giachetti; Claudio Luchinat; Giacomo Parigi; Maxim V Petoukhov; Roberta Pierattelli; Enrico Ravera; Dmitri I Svergun
Journal:  J Am Chem Soc       Date:  2010-09-29       Impact factor: 15.419

Review 3.  Structural characterization of proteins and complexes using small-angle X-ray solution scattering.

Authors:  Haydyn D T Mertens; Dmitri I Svergun
Journal:  J Struct Biol       Date:  2010-06-15       Impact factor: 2.867

4.  Validation of a lanthanide tag for the analysis of protein dynamics by paramagnetic NMR spectroscopy.

Authors:  Mathias A S Hass; Peter H J Keizers; Anneloes Blok; Yoshitaka Hiruma; Marcellus Ubbink
Journal:  J Am Chem Soc       Date:  2010-07-28       Impact factor: 15.419

5.  A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering.

Authors:  Pau Bernadó; Laurence Blanchard; Peter Timmins; Dominique Marion; Rob W H Ruigrok; Martin Blackledge
Journal:  Proc Natl Acad Sci U S A       Date:  2005-11-11       Impact factor: 11.205

6.  Refinement of multidomain protein structures by combination of solution small-angle X-ray scattering and NMR data.

Authors:  Alexander Grishaev; Justin Wu; Jill Trewhella; Ad Bax
Journal:  J Am Chem Soc       Date:  2005-11-30       Impact factor: 15.419

7.  Structural characterization of flexible proteins using small-angle X-ray scattering.

Authors:  Pau Bernadó; Efstratios Mylonas; Maxim V Petoukhov; Martin Blackledge; Dmitri I Svergun
Journal:  J Am Chem Soc       Date:  2007-04-06       Impact factor: 15.419

Review 8.  Analysis of X-ray and neutron scattering from biomacromolecular solutions.

Authors:  Maxim V Petoukhov; Dmitri I Svergun
Journal:  Curr Opin Struct Biol       Date:  2007-08-21       Impact factor: 6.809

9.  The eNMR platform for structural biology.

Authors:  Alexandre M J J Bonvin; Antonio Rosato; Tsjerk A Wassenaar
Journal:  J Struct Funct Genomics       Date:  2010-03-13

10.  Novel techniques for weak alignment of proteins in solution using chemical tags coordinating lanthanide ions.

Authors:  Takahisa Ikegami; Laurent Verdier; Peyman Sakhaii; Susanne Grimme; Barbara Pescatore; Krishna Saxena; Klaus M Fiebig; Christian Griesinger
Journal:  J Biomol NMR       Date:  2004-07       Impact factor: 2.835
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  14 in total

1.  Examination of matrix metalloproteinase-1 in solution: a preference for the pre-collagenolysis state.

Authors:  Linda Cerofolini; Gregg B Fields; Marco Fragai; Carlos F G C Geraldes; Claudio Luchinat; Giacomo Parigi; Enrico Ravera; Dmitri I Svergun; João M C Teixeira
Journal:  J Biol Chem       Date:  2013-09-11       Impact factor: 5.157

2.  Information content of long-range NMR data for the characterization of conformational heterogeneity.

Authors:  Witold Andrałojć; Konstantin Berlin; David Fushman; Claudio Luchinat; Giacomo Parigi; Enrico Ravera; Luca Sgheri
Journal:  J Biomol NMR       Date:  2015-06-05       Impact factor: 2.835

3.  FANTEN: a new web-based interface for the analysis of magnetic anisotropy-induced NMR data.

Authors:  Mauro Rinaldelli; Azzurra Carlon; Enrico Ravera; Giacomo Parigi; Claudio Luchinat
Journal:  J Biomol NMR       Date:  2014-11-22       Impact factor: 2.835

4.  Identification of productive and futile encounters in an electron transfer protein complex.

Authors:  Witold Andrałojć; Yoshitaka Hiruma; Wei-Min Liu; Enrico Ravera; Masaki Nojiri; Giacomo Parigi; Claudio Luchinat; Marcellus Ubbink
Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-21       Impact factor: 11.205

Review 5.  The dynamic duo: combining NMR and small angle scattering in structural biology.

Authors:  Janosch Hennig; Michael Sattler
Journal:  Protein Sci       Date:  2014-04-17       Impact factor: 6.725

6.  Structural characterization of a flexible two-domain protein in solution using small angle X-ray scattering and NMR data.

Authors:  Alexander Lemak; Bin Wu; Adelinda Yee; Scott Houliston; Hsiau-Wei Lee; Aleksandras Gutmanas; Xianyang Fang; Maite Garcia; Anthony Semesi; Yun-Xing Wang; James H Prestegard; Cheryl H Arrowsmith
Journal:  Structure       Date:  2014-11-06       Impact factor: 5.006

7.  Visualizing transient dark states by NMR spectroscopy.

Authors:  Nicholas J Anthis; G Marius Clore
Journal:  Q Rev Biophys       Date:  2015-02       Impact factor: 5.318

Review 8.  Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints.

Authors:  Xue-Ni Hou; Hidehito Tochio
Journal:  Biophys Rev       Date:  2022-01-11

9.  Prion Protein-Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering.

Authors:  Lester Carter; Seung Joong Kim; Dina Schneidman-Duhovny; Jan Stöhr; Guillaume Poncet-Montange; Thomas M Weiss; Hiro Tsuruta; Stanley B Prusiner; Andrej Sali
Journal:  Biophys J       Date:  2015-08-18       Impact factor: 4.033

10.  Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations.

Authors:  Witold Andrałojć; Enrico Ravera; Loïc Salmon; Giacomo Parigi; Hashim M Al-Hashimi; Claudio Luchinat
Journal:  Phys Chem Chem Phys       Date:  2016-02-17       Impact factor: 3.676
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