NMR paper Principal components analysis of protein structure ensembles calculated using NMR dat

		BioNMR > Educational resources > Journal club
[NMR paper] Principal components analysis of protein structure ensembles calculated using NMR dat

Webservers

NMR processing:

MDD

NMR assignment:

Backbone:

Side-chains:

NOEs:

Structure from NMR restraints:

Ab initio:

Fragment-based:

Rosetta-NMR (Robetta)

Template-based:

GeNMR

I-TASSER

Refinement:

Amber

Structure from chemical shifts:

Fragment-based:

Homology-based:

Torsion angles from chemical shifts:

Preditor

TALOS

Promega- Proline

Secondary structure from chemical shifts:

CSI (via RCI server)

TALOS

MICS caps, β-turns

d2D

PECAN

Flexibility from chemical shifts:

RCI

Interactions from chemical shifts:

HADDOCK

Chemical shifts re-referencing:

NMR model quality:

NOEs, other restraints:

Chemical shifts:

RDCs:

Pseudocontact shifts:

Protein geomtery:

SAVES2 or SAVES4

Quality Control Check

NMR spectrum prediction:

FANDAS

MestReS

V-NMR

Flexibility from structure:

Backbone S2

Methyl S2

B-factor

Molecular dynamics:

Gromacs

Amber

Antechamber

Chemical shifts prediction:

From structure:

Shiftx2

Sparta+

Camshift

CH3shift- Methyl

ArShift- Aromatic

ShiftS

Proshift

PPM

CheShift-2- Cα

From sequence:

Shifty

Camcoil

Poulsen_rc_CS

Disordered proteins:

MAXOCC

Format conversion & validation:

CCPN

From NMR-STAR 3.1

Validate NMR-STAR 3.1

NMR sample preparation:

Protein disorder:

DisMeta

Protein solubility:

Isotope labeling:

Solid-state NMR:

Thread Tools

Search this Thread

Rate Thread

Display Modes

11-19-2010, 08:32 PM

nmrlearner

Senior Member

Join Date: Jan 2005

Posts: 23,732

Points: 193,617, Level: 100

Level up: 0%, 0 Points needed

Activity: 50.7%

Last Achievements

Award-Showcase

NMR Credits: 0

NMR Points: 193,617

Downloads: 0

Uploads: 0

Principal components analysis of protein structure ensembles calculated using NMR dat

Principal components analysis of protein structure ensembles calculated using NMR data.

Related Articles Principal components analysis of protein structure ensembles calculated using NMR data.

J Biomol NMR. 2001 May;20(1):61-70

Authors: Howe PW

One important problem when calculating structures of biomolecules from NMR data is distinguishing converged structures from outlier structures. This paper describes how Principal Components Analysis (PCA) has the potential to classify calculated structures automatically, according to correlated structural variation across the population. PCA analysis has the additional advantage that it highlights regions of proteins which are varying across the population. To apply PCA, protein structures have to be reduced in complexity and this paper describes two different representations of protein structures which achieve this. The calculated structures of a 28 amino acid peptide are used to demonstrate the methods. The two different representations of protein structure are shown to give equivalent results, and correct results are obtained even though the ensemble of structures used as an example contains two different protein conformations. The PCA analysis also correctly identifies the structural differences between the two conformations.

PMID: 11430756 [PubMed - indexed for MEDLINE]

Source: PubMed

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Local protein backbone folds determined by calculated NMR chemical shifts. Local protein backbone folds determined by calculated NMR chemical shifts. Local protein backbone folds determined by calculated NMR chemical shifts. J Comput Chem. 2011 Sep 9; Authors: Czajlik A, Hudáky I, Perczel A Abstract NMR chemical shifts (CSs: ?N(NH) , ?C(?) , ?C(?) , ?C', ?H(NH) , and ?H(?) ) were computed for the amino acid backbone conformers (?(L) , ?(L) , ?(L) , ?(L) , ?(L) , ?(D) , ?(D) , ?(D) , and ?(D) ) modeled by oligoalanine structures. Topological differences of the extended fold were investigated on single ?-strands,...	nmrlearner	Journal club	0	09-10-2011 06:51 PM
Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions. Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions. Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions. BMC Struct Biol. 2011 May 12;11(1):24 Authors: Isvoran A, Badel A, Craescu CT, Miron S, Miteva MA ABSTRACT: BACKGROUND: Disrupting protein-protein interactions by small organic molecules is nowadays a promising strategy employed to block protein targets involved in different pathologies. However, structural...	nmrlearner	Journal club	0	05-17-2011 06:21 PM
Wavelet transform analysis of NMR structure ensembles to reveal internal fluctuations of enzymes. Wavelet transform analysis of NMR structure ensembles to reveal internal fluctuations of enzymes. Wavelet transform analysis of NMR structure ensembles to reveal internal fluctuations of enzymes. Amino Acids. 2011 Apr 9; Authors: Hu M, Li Y, Yang G, Li G, Li M, Wen Z Internal motions and flexibility are essential for biological functions in proteins. To assess the internal fluctuations and conformational flexibility of proteins, reliable computational methods are needed. In this study, wavelet transformation was used to filter out the noise and...	nmrlearner	Journal club	0	04-12-2011 11:08 AM
High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations High-resolution protein structure determination starting with a global fold calculated from exact solutions to the RDC equations Abstract We present a novel structure determination approach that exploits the global orientational restraints from RDCs to resolve ambiguous NOE assignments. Unlike traditional approaches that bootstrap the initial fold from ambiguous NOE assignments, we start by using RDCs to compute accurate secondary structure element (SSE) backbones at the beginning of structure calculation. Our structure determination package, called rdc-Panda (RDC-based SSE PAcking with...	nmrlearner	Journal club	0	01-09-2011 12:46 PM
[NMR paper] NMR structural analysis of alpha-bungarotoxin and its complex with the principal alph NMR structural analysis of alpha-bungarotoxin and its complex with the principal alpha-neurotoxin-binding sequence on the alpha 7 subunit of a neuronal nicotinic acetylcholine receptor. Related Articles NMR structural analysis of alpha-bungarotoxin and its complex with the principal alpha-neurotoxin-binding sequence on the alpha 7 subunit of a neuronal nicotinic acetylcholine receptor. J Biol Chem. 2002 Apr 5;277(14):12406-17 Authors: Moise L, Piserchio A, Basus VJ, Hawrot E We report a new, higher resolution NMR structure of...	nmrlearner	Journal club	0	11-24-2010 08:49 PM
[NMR paper] The electric dipole moment of DNA-binding HU protein calculated by the use of an NMR The electric dipole moment of DNA-binding HU protein calculated by the use of an NMR database. Related Articles The electric dipole moment of DNA-binding HU protein calculated by the use of an NMR database. Biophys Chem. 1999 Aug 30;80(3):153-63 Authors: Takashima S, Yamaoka K Electric birefringence measurements indicated the presence of a large permanent dipole moment in HU protein-DNA complex. In order to substantiate this observation, numerical computation of the dipole moment of HU protein homodimer was carried out by using NMR protein...	nmrlearner	Journal club	0	11-18-2010 08:31 PM
Structure-based protein NMR assignments using native structural ensembles Structure-based protein NMR assignments using native structural ensembles Mehmet Serkan Apaydın, Vincent Conitzer and Bruce Randall Donald Journal of Biomolecular NMR; 2008; 40(4); pp 263-276 Abstract: An important step in NMR protein structure determination is the assignment of resonances and NOEs to corresponding nuclei. Structure-based assignment (SBA) uses a model structure (“template”) for the target protein to expedite this process. Nuclear vector replacement (NVR) is an SBA framework that combines multiple sources of NMR data (chemical shifts, RDCs, sparse NOEs, amide exchange...	matthias	Journal club	0	08-14-2008 12:54 AM
Programs for alignment of protein NMR ensembles If you need to align models in your NMR ensemble, you can use the following programs to do so. MolMol - Official website - Linux binaries from Patrick Finerty website - BioXRay distribution SuperPose server Suppose	nmrlearner	Structural analysis	0	09-14-2005 07:04 PM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off