Literature DB >> 19739624

Fast and accurate predictions of protein NMR chemical shifts from interatomic distances.

Kai J Kohlhoff1, Paul Robustelli, Andrea Cavalli, Xavier Salvatella, Michele Vendruscolo.   

Abstract

We present a method, CamShift, for the rapid and accurate prediction of NMR chemical shifts from protein structures. The calculations performed by CamShift are based on an approximate expression of the chemical shifts in terms of polynomial functions of interatomic distances. Since these functions are very fast to compute and readily differentiable, the CamShift approach can be utilized in standard protein structure calculation protocols.

Mesh:

Substances:

Year:  2009        PMID: 19739624     DOI: 10.1021/ja903772t

Source DB:  PubMed          Journal:  J Am Chem Soc        ISSN: 0002-7863            Impact factor:   15.419


  100 in total

1.  Long-timescale molecular-dynamics simulations of the major urinary protein provide atomistic interpretations of the unusual thermodynamics of ligand binding.

Authors:  Julie Roy; Charles A Laughton
Journal:  Biophys J       Date:  2010-07-07       Impact factor: 4.033

2.  A probabilistic approach for validating protein NMR chemical shift assignments.

Authors:  Bowei Wang; Yunjun Wang; David S Wishart
Journal:  J Biomol NMR       Date:  2010-05-06       Impact factor: 2.835

3.  Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction.

Authors:  Juuso Lehtivarjo; Kari Tuppurainen; Tommi Hassinen; Reino Laatikainen; Mikael Peräkylä
Journal:  J Biomol NMR       Date:  2012-03       Impact factor: 2.835

4.  Following easy slope paths on a free energy landscape: the case study of the Trp-cage folding mechanism.

Authors:  Fabrizio Marinelli
Journal:  Biophys J       Date:  2013-09-03       Impact factor: 4.033

5.  4D prediction of protein (1)H chemical shifts.

Authors:  Juuso Lehtivarjo; Tommi Hassinen; Samuli-Petrus Korhonen; Mikael Peräkylä; Reino Laatikainen
Journal:  J Biomol NMR       Date:  2009-10-30       Impact factor: 2.835

Review 6.  Chemical shifts in biomolecules.

Authors:  David A Case
Journal:  Curr Opin Struct Biol       Date:  2013-02-17       Impact factor: 6.809

7.  HASH: a program to accurately predict protein Hα shifts from neighboring backbone shifts.

Authors:  Jianyang Zeng; Pei Zhou; Bruce Randall Donald
Journal:  J Biomol NMR       Date:  2012-12-16       Impact factor: 2.835

8.  Free-Energy Landscape of the Amino-Terminal Fragment of Huntingtin in Aqueous Solution.

Authors:  Vincent Binette; Sébastien Côté; Normand Mousseau
Journal:  Biophys J       Date:  2016-03-08       Impact factor: 4.033

9.  PACSY, a relational database management system for protein structure and chemical shift analysis.

Authors:  Woonghee Lee; Wookyung Yu; Suhkmann Kim; Iksoo Chang; Weontae Lee; John L Markley
Journal:  J Biomol NMR       Date:  2012-08-19       Impact factor: 2.835

10.  Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field.

Authors:  Shuxiang Li; Casey T Andrews; Tamara Frembgen-Kesner; Mark S Miller; Stephen L Siemonsma; Timothy D Collingsworth; Isaac T Rockafellow; Nguyet Anh Ngo; Brady A Campbell; Reid F Brown; Chengxuan Guo; Michael Schrodt; Yu-Tsan Liu; Adrian H Elcock
Journal:  J Chem Theory Comput       Date:  2015-03-10       Impact factor: 6.006

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.