scholarly journals Simultaneous Assignment and Structure Determination of Proteins From Sparsely Labeled NMR Datasets

2021 ◽  
Vol 8 ◽  
Author(s):  
Arup Mondal ◽  
Alberto Perez
Keyword(s):  
Bayesian Approach ◽  
Structure Determination ◽  
Structure Prediction ◽  
Critical Assessment ◽  
Limited Data ◽  
Computational Tools ◽  
Nmr Data

Sparsely labeled NMR samples provide opportunities to study larger biomolecular assemblies than is traditionally done by NMR. This requires new computational tools that can handle the sparsity and ambiguity in the NMR datasets. The MELD (modeling employing limited data) Bayesian approach was assessed to be the best performing in predicting structures from sparsely labeled NMR data in the 13th edition of the Critical Assessment of Structure Prediction (CASP) event—and limitations of the methodology were also noted. In this report, we evaluate the nature and difficulty in modeling unassigned sparsely labeled NMR datasets and report on an improved methodological pipeline leading to higher-accuracy predictions. We benchmark our methodology against the NMR datasets provided by CASP 13.

scholarly journals Structure determination of a new protein from backbone-centered NMR data and NMR-assisted structure prediction

2006 ◽  
Vol 65 (2) ◽  
pp. 480-489 ◽  
Author(s):  
K. L. Mayer ◽  
Y. Qu ◽  
S. Bansal ◽  
P. D. LeBlond ◽  
F. E. Jenney ◽  
...  
Keyword(s):  
Structure Determination ◽  
Structure Prediction ◽  
Nmr Data ◽  
New Protein

Computational structure determination of novel metal–organic frameworks

2018 ◽  
Vol 54 (77) ◽  
pp. 10812-10815 ◽  
Author(s):  
Mohammad Wahiduzzaman ◽  
Sujing Wang ◽  
Benjamin J. Sikora ◽  
Christian Serre ◽  
Guillaume Maurin
Keyword(s):  
Structure Determination ◽  
Structure Prediction ◽  
Metal Organic Frameworks ◽  
Prediction Tool ◽  
Computational Structure ◽  
Metal Organic

A structure prediction tool has been developed to guide the discovery of MOF materials.

scholarly journals Blind protein structure prediction using accelerated free-energy simulations

2016 ◽  
Vol 2 (11) ◽  
pp. e1601274 ◽  
Author(s):  
Alberto Perez ◽  
Joseph A. Morrone ◽  
Emiliano Brini ◽  
Justin L. MacCallum ◽  
Ken A. Dill
Keyword(s):  
Molecular Dynamics ◽  
Structure Prediction ◽  
Protein Structures ◽  
Critical Assessment ◽  
Dynamics Simulation ◽  
Limited Data ◽  
Native Protein ◽  
Acceleration Method ◽  
Energy Simulations ◽  
Proof Of Principle

We report a key proof of principle of a new acceleration method [Modeling Employing Limited Data (MELD)] for predicting protein structures by molecular dynamics simulation. It shows that such Boltzmann-satisfying techniques are now sufficiently fast and accurate to predict native protein structures in a limited test within the Critical Assessment of Structure Prediction (CASP) community-wide blind competition.

CMPZ– an algorithm for the efficient comparison of periodic structures

2006 ◽  
Vol 39 (1) ◽  
pp. 6-16 ◽  
Author(s):  
R. Hundt ◽  
J. C. Schön ◽  
M. Jansen
Keyword(s):  
Structure Determination ◽  
Atomic Structure ◽  
Structure Prediction ◽  
Materials Science ◽  
Periodic Structures ◽  
Analysis Program ◽  
Systematic Comparison ◽  
Point Patterns ◽  
Solid Compounds

The systematic comparison of the atomic structure of solid compounds has become an important task in crystallography, chemistry, physics and materials science, in particular in the context of structure prediction and structure determination of crystalline solids. In this work, an efficient and robust algorithm for the comparison of periodic structures is presented, which is based on the mapping of the point patterns of the two structures into each other. This algorithm has been implemented as the moduleCMPZin the structure visualization and analysis programKPLOT.

Reaktion von 1.4-Dienen mit Metallkomplexen, I Darstellung und Röntgenstrukturanalyse eines π-enyl-Komplexes der Zusammensetzung (C8H13PdCl)2/ Reaction of 1,4-Dienes with Metal Complexes, I Synthesis and X-ray Structure Determination of a π-enyl Complex of Composition (C8H18PdCl)2

1976 ◽  
Vol 31 (4) ◽  
pp. 455-462 ◽  
Author(s):  
Peter Feldhaus ◽  
Richard Ratka ◽  
Hermann Schmid ◽  
Manfred L. Ziegler
Keyword(s):  
Metal Complexes ◽  
Structure Determination ◽  
Three Dimensional ◽  
Fourier Methods ◽  
X Ray ◽  
H Nmr ◽  
Nmr Data ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

Reaction of (C6H5CN)2PdCl2 and 1,3-dimethylenecyclohexane led to an exocyclic π-enyl complex of formula (C8H13PdCl)2-bis(η3-2-methylene-6-methylcyclohexyl)(di-µ-chloro)-dipalladium. IR and 1H NMR data are in agreement with this formulation.The compound is monoclinic, with unit cell dimensions α = 499.97 ± 0.08, b =1342.26 ± 0.19, c =1379.60 ± 0.20 pm, β = 99.43 ± 0.02°, space group C5h2-P21/C, Ζ = 2, dX-ray = 1.83 g/cm3.The structure was determined from three-dimensional X-ray data by Patterson and Fourier methods. Least squares refinement by use of 1045 independent reflections has reached R1 = 5.6%.

Potential Anticancer Agents, XI. X-Ray Structure Determination of Acantholide [1]

1979 ◽  
Vol 34 (9-10) ◽  
pp. 677-682 ◽  
Author(s):  
H. Lotter ◽  
H. Wagner ◽  
A. A. Saleh ◽  
G. A. Cordell ◽  
N. R. Famsworth
Keyword(s):  
Solid State ◽  
Antitumor Activity ◽  
Sesquiterpene Lactone ◽  
Anticancer Agents ◽  
Structure Determination ◽  
Direct Methods ◽  
X Ray ◽  
Activity Evaluation ◽  
Nmr Data

Abstract The X-ray structure of acantholide, a melampolide sesquiterpene lactone from Acanthosper­mum glabratum (D C .) Willd. was determined by the aid of direct methods. The compound was cy­totoxic but displayed no antitumor activity. Evaluation of the X-ray and NMR data indicated that the same conformation exists in the solid state as in solution.

scholarly journals Extending the applicability of P3D for structure determination of small molecules

2021 ◽  
Vol 2 (1) ◽  
pp. 105-116
Author(s):  
Alain Ibáñez de Opakua ◽  
Markus Zweckstetter
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Small Molecules ◽  
Structure Determination ◽  
Structural Characteristics ◽  
Discrimination Power ◽  
Nmr Parameters ◽  
Structural Assignment ◽  
Nmr Data

Abstract. The application of anisotropic nuclear magnetic resonance (NMR) parameters for the correct structural assignment of small molecules requires the use of partially ordered media. Previously we demonstrated that the use of P3D simulations using poly(γ-benzyl-L-glutamate) (PBLG) as an alignment medium allows for the determination of the correct diastereomer from extremely sparse NMR data. Through the analysis of the structural characteristics of small molecules in different alignment media, here we show that when steric or electrostatic factors dominate the alignment, P3D-PBLG retains its diastereomer discrimination power. We also demonstrate that P3D simulations can define the different conformations of a flexible small molecule from sparse NMR data.

scholarly journals Crystal structure determination of an elusive methanol solvate – hydrate of catechin using crystal structure prediction and NMR crystallography

CrystEngComm ◽  
2020 ◽  
Vol 22 (30) ◽  
pp. 4969-4981 ◽  
Author(s):  
Marta K. Dudek ◽  
Piotr Paluch ◽  
Justyna Śniechowska ◽  
Karol P. Nartowski ◽  
Graeme M. Day ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structure Determination ◽  
Structure Prediction ◽  
Crystal Structure Determination ◽  
Crystal Structure Prediction ◽  
Molecular Conformations ◽  
Nmr Crystallography

A useful short-cut was developed to limit the number of molecular conformations that need to be regarded in crystal structure prediction calculations, which led to the crystal structure determination of new methanol solvate – hydrate of catechin.

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