NDLI: A robust algorithm for optimizing protein structures with NMR chemical shifts

Content Provider	Springer Nature Link
Author	Berjanskii, Mark Arndt, David Liang, Yongjie Wishart, David S.
Copyright Year	2015
Abstract	Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and “PDB worthy”. The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca .
Starting Page	255
Ending Page	264
Page Count	10
File Format	PDF
ISSN	09252738
Journal	Journal of Biomolecular NMR
Volume Number	63
Issue Number	3
e-ISSN	15735001
Language	English
Publisher	Springer Netherlands
Publisher Date	2015-09-07
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Protein Structure Accuracy NMR Chemical shifts Biophysics and Biological Physics Biochemistry Spectroscopy/Spectrometry
Content Type	Text
Resource Type	Article
Subject	Spectroscopy Biochemistry

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

An overview of tools for the validation of protein NMR structures

Automated assignment of NMR chemical shifts based on a known structure and 4D spectra

Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker

Nucleic acid helix structure determination from NMR proton chemical shifts

RASP: rapid and robust backbone chemical shift assignments from protein structure

Robust structure-based resonance assignment for functional protein studies by NMR

Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3

Type I and II β-turns prediction using NMR chemical shifts

Accessible surface area from NMR chemical shifts

A robust algorithm for optimizing protein structures with NMR chemical shifts

Similar Documents

An overview of tools for the validation of protein NMR structures

Automated assignment of NMR chemical shifts based on a known structure and 4D spectra

Improved chemical shift based fragment selection for CS-Rosetta using Rosetta3 fragment picker

Nucleic acid helix structure determination from NMR proton chemical shifts

RASP: rapid and robust backbone chemical shift assignments from protein structure

Robust structure-based resonance assignment for functional protein studies by NMR

Analysis of the performance of the CHESHIRE and YAPP methods at CASD-NMR round 3

Type I and II β-turns prediction using NMR chemical shifts

Accessible surface area from NMR chemical shifts

A robust algorithm for optimizing protein structures with NMR chemical shifts