Literature DB >> 25855813

WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics.

Christopher J Knight1, Jochen S Hub2.   

Abstract

Small- and wide-angle X-ray scattering (SWAXS) has evolved into a powerful tool to study biological macromolecules in solution. The interpretation of SWAXS curves requires their accurate predictions from structural models. Such predictions are complicated by scattering contributions from the hydration layer and by effects from thermal fluctuations. Here, we describe the new web server WAXSiS (WAXS in solvent) that computes SWAXS curves based on explicit-solvent all-atom molecular dynamics (MD) simulations (http://waxsis.uni-goettingen.de/). The MD simulations provide a realistic model for both the hydration layer and the excluded solvent, thereby avoiding any solvent-related fitting parameters, while naturally accounting for thermal fluctuations.
© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Year:  2015        PMID： 25855813      PMCID： PMC4489308          DOI： 10.1093/nar/gkv309

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  19 in total

1.  Is the first hydration shell of lysozyme of higher density than bulk water?

Authors:  Franci Merzel; Jeremy C Smith
Journal:  Proc Natl Acad Sci U S A       Date:  2002-04-16       Impact factor: 11.205

2.  A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

Authors:  Yong Duan; Chun Wu; Shibasish Chowdhury; Mathew C Lee; Guoming Xiong; Wei Zhang; Rong Yang; Piotr Cieplak; Ray Luo; Taisung Lee; James Caldwell; Junmei Wang; Peter Kollman
Journal:  J Comput Chem       Date:  2003-12       Impact factor: 3.376

3.  Simulated x-ray scattering of protein solutions using explicit-solvent models.

Authors:  Sanghyun Park; Jaydeep P Bardhan; Benoît Roux; Lee Makowski
Journal:  J Chem Phys       Date:  2009-04-07       Impact factor: 3.488

Review 4.  X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.

Authors:  Christopher D Putnam; Michal Hammel; Greg L Hura; John A Tainer
Journal:  Q Rev Biophys       Date:  2007-08       Impact factor: 5.318

Review 5.  Impact and progress in small and wide angle X-ray scattering (SAXS and WAXS).

Authors:  Melissa A Graewert; Dmitri I Svergun
Journal:  Curr Opin Struct Biol       Date:  2013-07-05       Impact factor: 6.809

Review 6.  Time-resolved structural studies at synchrotrons and X-ray free electron lasers: opportunities and challenges.

Authors:  Richard Neutze; Keith Moffat
Journal:  Curr Opin Struct Biol       Date:  2012-09-25       Impact factor: 6.809

7.  SASBDB, a repository for biological small-angle scattering data.

Authors:  Erica Valentini; Alexey G Kikhney; Gianpietro Previtali; Cy M Jeffries; Dmitri I Svergun
Journal:  Nucleic Acids Res       Date:  2014-10-28       Impact factor: 16.971

8.  FoXS: a web server for rapid computation and fitting of SAXS profiles.

Authors:  Dina Schneidman-Duhovny; Michal Hammel; Andrej Sali
Journal:  Nucleic Acids Res       Date:  2010-05-27       Impact factor: 16.971

9.  AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models.

Authors:  Frédéric Poitevin; Henri Orland; Sebastian Doniach; Patrice Koehl; Marc Delarue
Journal:  Nucleic Acids Res       Date:  2011-06-10       Impact factor: 16.971

Review 10.  Reconstruction of SAXS Profiles from Protein Structures.

Authors:  Daniel K Putnam; Edward W Lowe; Jens Meiler
Journal:  Comput Struct Biotechnol J       Date:  2013-11-26       Impact factor: 7.271
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  41 in total

1.  Structural Characterization of N-WASP Domain V Using MD Simulations with NMR and SAXS Data.

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Journal:  Biophys J       Date:  2019-02-26       Impact factor: 4.033

2.  D+: software for high-resolution hierarchical modeling of solution X-ray scattering from complex structures.

Authors:  Avi Ginsburg; Tal Ben-Nun; Roi Asor; Asaf Shemesh; Lea Fink; Roee Tekoah; Yehonatan Levartovsky; Daniel Khaykelson; Raviv Dharan; Amos Fellig; Uri Raviv
Journal:  J Appl Crystallogr       Date:  2019-02-01       Impact factor: 3.304

Review 3.  The role of small-angle scattering in structure-based screening applications.

Authors:  Po-Chia Chen; Janosch Hennig
Journal:  Biophys Rev       Date:  2018-10-10

4.  Disentangling polydispersity in the PCNA-p15PAF complex, a disordered, transient and multivalent macromolecular assembly.

Authors:  Tiago N Cordeiro; Po-Chia Chen; Alfredo De Biasio; Nathalie Sibille; Francisco J Blanco; Jochen S Hub; Ramon Crehuet; Pau Bernadó
Journal:  Nucleic Acids Res       Date:  2017-02-17       Impact factor: 16.971

5.  HullRad: Fast Calculations of Folded and Disordered Protein and Nucleic Acid Hydrodynamic Properties.

Authors:  Patrick J Fleming; Karen G Fleming
Journal:  Biophys J       Date:  2018-02-27       Impact factor: 4.033

6.  Recent advances in the UltraScan SOlution MOdeller (US-SOMO) hydrodynamic and small-angle scattering data analysis and simulation suite.

Authors:  Emre Brookes; Mattia Rocco
Journal:  Eur Biophys J       Date:  2018-03-28       Impact factor: 1.733

7.  High-Resolution Structures of the Amyloid-β 1-42 Dimers from the Comparison of Four Atomistic Force Fields.

Authors:  Viet Hoang Man; Phuong H Nguyen; Philippe Derreumaux
Journal:  J Phys Chem B       Date:  2017-06-07       Impact factor: 2.991

8.  Salt Dependence of A-Form RNA Duplexes: Structures and Implications.

Authors:  Yen-Lin Chen; Lois Pollack
Journal:  J Phys Chem B       Date:  2019-11-11       Impact factor: 2.991

9.  Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations.

Authors:  Suzette A Pabit; Andrea M Katz; Igor S Tolokh; Aleksander Drozdetski; Nathan Baker; Alexey V Onufriev; Lois Pollack
Journal:  J Chem Phys       Date:  2016-05-28       Impact factor: 3.488

10.  SAXS/SANS on Supercharged Proteins Reveals Residue-Specific Modifications of the Hydration Shell.

Authors:  Henry S Kim; Anne Martel; Eric Girard; Martine Moulin; Michael Härtlein; Dominique Madern; Martin Blackledge; Bruno Franzetti; Frank Gabel
Journal:  Biophys J       Date:  2016-05-24       Impact factor: 4.033
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