Low Mode Search. An Efficient, Automated Computational Method for Conformational Analysis:  Application to Cyclic and Acyclic Alkanes and Cyclic Peptides

1996 ◽  
Vol 118 (21) ◽  
pp. 5011-5019 ◽  
Author(s):  
István Kolossváry ◽  
Wayne C. Guida
Keyword(s):  
Conformational Analysis ◽  
Cyclic Peptides ◽  
Computational Method ◽  
Analysis Application

Conformational Analysis of SomeC2-Symmetric Cyclic Peptides Containing Tetrahydrofuran Amino Acids†

2006 ◽  
Vol 71 (16) ◽  
pp. 6240-6243 ◽  
Author(s):  
Tushar Kanti Chakraborty ◽  
Saumya Roy ◽  
Dipankar Koley ◽  
Samit Kumar Dutta ◽  
Ajit Chand Kunwar
Keyword(s):  
Amino Acids ◽  
Conformational Analysis ◽  
Cyclic Peptides

Toward structure prediction of cyclic peptides

2015 ◽  
Vol 17 (6) ◽  
pp. 4210-4219 ◽  
Author(s):  
Hongtao Yu ◽  
Yu-Shan Lin
Keyword(s):  
Structure Prediction ◽  
Cyclic Peptides ◽  
Computational Method ◽  
Structural Description

A computational method to provide a converged structural description for cyclic peptides.

Conformational analysis and structure elucidation of 2,3-dimethyl- and 2,4-dimethyl-2,4-hexadienes by AM1 and He(I) ultraviolet photoelectron spectroscopy

1990 ◽  
Vol 68 (11) ◽  
pp. 2078-2084 ◽  
Author(s):  
N. H. Werstiuk ◽  
K. B. Clark ◽  
W. J. Leigh
Keyword(s):  
Conformational Analysis ◽  
Electronic Properties ◽  
Photoelectron Spectroscopy ◽  
Structure Elucidation ◽  
Computational Method ◽  
Ultraviolet Photoelectron Spectroscopy

A study of (E)-2,3-dimethyl-2,4-hexadiene (E-3) and (Z)-2,3-dimethyl-2,4-hexadiene (Z-3) by the semiempirical computational method AM1 and He(I) ultraviolet photoelectron spectroscopy (UPS) has established that this combination of AM1/UPS will be generally useful for detailing conformational and electronic properties of alkyl-substituted 1,3-dienes. This method was used to elucidate the structures of the stereoisomeric 2,4-dimefhyl-2,4-hexadienes obtained from the photolysis of 1,3,3,4-tetramethylcyclobutene (2). Keywords: 2,3- and 2,4-dimethyl-2,4-hexadienes, conformational analysis, AM1, He(I) photoelectron spectroscopy.

Cyclic peptides from the ascidian Lissoclinum patella: conformational analysis of patellamide D by x-ray analysis and molecular modeling

1989 ◽  
Vol 54 (14) ◽  
pp. 3463-3472 ◽  
Author(s):  
Francis J. Schmitz ◽  
Mohamad B. Ksebati ◽  
James S. Chang ◽  
J. L. Wang ◽  
M. Bilayet Hossain ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Conformational Analysis ◽  
Cyclic Peptides ◽  
X Ray ◽  
Lissoclinum Patella

scholarly journals APPTEST is an innovative new method for the automatic prediction of peptide tertiary structures

2021 ◽  
Author(s):  
Patrick Brendan Timmons ◽  
Chandralal M. Hewage
Keyword(s):  
Network Architecture ◽  
Structure Prediction ◽  
Cyclic Peptides ◽  
Tertiary Structure ◽  
Prediction Method ◽  
Computational Method ◽  
Computationally Efficient ◽  
Biological Targets ◽  
Benchmark Datasets ◽  
Natural Amino Acids

AbstractGood knowledge of a peptide’s tertiary structure is important for understanding its function and its interactions with its biological targets. APPTEST is a novel computational method that employs a neural network architecture and simulated annealing methods for the prediction of peptide tertiary structure from the primary sequence. APPTEST works for both linear and cyclic peptides of 5-40 natural amino acids. APPTEST is computationally efficient, returning predicted structures within a number of minutes. APPTEST performance was evaluated on a set of 356 test peptides; the best structure predicted for each peptide deviated by an average of 1.9Å from its experimentally determined backbone conformation, and a native or near-native structure was predicted for 97% of the target sequences. A comparison of APPTEST performance with PEP-FOLD, PEPstrMOD and Peplook across benchmark datasets of short, long and cyclic peptides shows that on average APPTEST produces structures more-native than the existing methods in all three categories. This innovative, cutting-edge peptide structure prediction method is available as an online web server at https://research.timmons.eu/apptest, facilitating in silico study and design of peptides by the wider research community.

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