Assessment of protein models with three-dimensional profiles

Nature ◽  
1992 ◽  
Vol 356 (6364) ◽  
pp. 83-85 ◽  
Author(s):  
Roland Lüthy ◽  
James U. Bowie ◽  
David Eisenberg
Keyword(s):  
Three Dimensional ◽  
Protein Models

Identifying Errors in Three-Dimensional Protein Models

2003 ◽  
pp. 277-313 ◽  
Author(s):  
Brian Marsden ◽  
Ruben Abagyan
Keyword(s):  
Three Dimensional ◽  
Protein Models

STUDIES OF FINDING LOW ENERGY CONFIGURATIONS IN OFF-LATTICE PROTEIN MODELS

2006 ◽  
Vol 05 (03) ◽  
pp. 587-594 ◽  
Author(s):  
JINGFA LIU ◽  
WENQI HUANG
Keyword(s):  
Lower Energy ◽  
Gradient Descent ◽  
Energy Landscape ◽  
Three Dimensional ◽  
Ground States ◽  
Low Energy ◽  
Protein Models ◽  
Energy Configurations ◽  
Energy Landscape Paving ◽  
Lattice Protein Models

We studied two three-dimensional off-lattice protein models with two species of monomers, hydrophobic and hydrophilic. Low energy configurations in both models were optimized using the energy landscape paving (ELP) method and subsequent gradient descent. The numerical results show that the proposed methods are very promising for finding the ground states of proteins. For all sequences with lengths 13 ≤ n ≤ 55, the algorithm finds states with lower energy than previously proposed putative ground states.

COMPUTER SIMULATION OF BIOLOGICAL MACROMOLECULES IN GENERALIZED ENSEMBLES

1999 ◽  
Vol 10 (08) ◽  
pp. 1521-1530 ◽  
Author(s):  
ULRICH H. E. HANSMANN
Keyword(s):  
Computer Simulation ◽  
Protein Folding ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Biological Macromolecules ◽  
Three Dimensional Structure ◽  
Ensemble Techniques ◽  
Folding Simulations ◽  
Protein Models ◽  
Structure Of Proteins

For many years the emphasis in protein-folding simulations has been laid as to how to predict the three-dimensional structure of proteins. Only recently has there be a shift in interest towards the thermodynamics of folding. We show that generalized-ensemble techniques are well suited to study both questions for realistic protein models.

scholarly journals Genome Organization, Phylogenies, Expression Patterns, and Three-Dimensional Protein Models of Two Acetylcholinesterase Genes from the Red Flour Beetle

PLoS ONE ◽  
2012 ◽  
Vol 7 (2) ◽  
pp. e32288 ◽  
Author(s):  
Yanhui Lu ◽  
Yuan-Ping Pang ◽  
Yoonseong Park ◽  
Xiwu Gao ◽  
Jianxiu Yao ◽  
...  
Keyword(s):  
Genome Organization ◽  
Expression Patterns ◽  
Three Dimensional ◽  
Red Flour Beetle ◽  
Flour Beetle ◽  
Protein Models

scholarly journals Vibrational spectroscopy and computer modeling of proteins: solving structure of α1-acid glycoprotein

2004 ◽  
Vol 18 (2) ◽  
pp. 323-330 ◽  
Author(s):  
Vladimír Kopecký ◽  
Rüdiger Ettrich ◽  
Kateřina Hofbauerová ◽  
Vladimír Baumruk
Keyword(s):  
Vibrational Spectroscopy ◽  
Preliminary Analysis ◽  
Three Dimensional ◽  
Nmr Analysis ◽  
New Approach ◽  
X Ray ◽  
Acid Glycoprotein ◽  
High Carbohydrate ◽  
Unknown Structure ◽  
Protein Models

This work introduces a new approach connecting vibrational spectroscopy with homology and energetic molecular modeling of proteins. Combination of both methods can compensate their disadvantages and result in realistic three-dimensional protein models. The approach is most powerful for membrane proteins or glycoproteins with high carbohydrate content where X-ray or NMR analysis is not always successful. Nevertheless, it can also serve as a tool of preliminary analysis of any protein with unknown structure. Power of the approach is demonstrated on human α1-acid glycoprotein. Its predicted structure published in [V. Kopecký Jr. et al.,Biochem. Biophys. Res. Commun.300(2003), 41–46] is discussed in detail with respect to the approach and its general employment.

scholarly journals Modeling of allergen proteins found in sea food products

2012 ◽  
Vol 32 (2) ◽  
pp. 393-400
Author(s):  
Nataly Galán-Freyle ◽  
Jesús Olivero-Verbel ◽  
Liney Díaz-López
Keyword(s):  
Immunoglobulin E ◽  
Three Dimensional ◽  
3D Models ◽  
Food Allergies ◽  
Alpha Helices ◽  
High Propensity ◽  
Hydrophobic Amino Acids ◽  
Protein Models ◽  
Mollusk Species ◽  
Sequence Similarities

Shellfish are a source of food allergens, and their consumption is the cause of severe allergic reactions in humans. Tropomyosins, a family of muscle proteins, have been identified as the major allergens in shellfish and mollusks species. Nevertheless, few experimentally determined three-dimensional structures are available in the Protein Data Base (PDB). In this study, 3D models of several homologous of tropomyosins present in marine shellfish and mollusk species (Chaf 1, Met e1, Hom a1, Per v1, and Pen a1) were constructed, validated, and their immunoglobulin E binding epitopes were identified using bioinformatics tools. All protein models for these allergens consisted of long alpha-helices. Chaf 1, Met e1, and Hom a1 had six conserved regions with sequence similarities to known epitopes, whereas Per v1 and Pen a1 contained only one. Lipophilic potentials of identified epitopes revealed a high propensity of hydrophobic amino acids in the immunoglobulin E binding site. This information could be useful to design tropomyosin-specific immunotherapy for sea food allergies.

scholarly journals CONSTRUCTION OF COMPUTATIONAL 3D STRUCTURES OF PROTEIN DRUG TARGETS OF MYCOBACTERIUM TUBERCULOSIS

2020 ◽  
pp. 82-85
Author(s):  
SUDHIR RAO ◽  
MISBAH SAYEEDA ◽  
TEJASHREE PRAKASH ◽  
PADMASHREE AP ◽  
SABIA IMRAN ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Drug Design ◽  
Drug Targets ◽  
Sequence Similarity ◽  
Three Dimensional ◽  
Homology Model ◽  
Public Access ◽  
Online Database ◽  
Different Strains ◽  
Protein Models

Objective: This study aims in constructing a three-dimensional modeled protein structure of potential drug targets in Mycobacterium tuberculosis bacteria. Methods: The protein models were constructed using SWISS-Model online tool. The constructed protein models were submitted in online database called Protein Model Database (PMDB) for public access to the structures. Results: A total of 100 protein sequences of M. tuberculosis were retrieved from UniProt database and were subjected for sequence similarity search and homology model construction. The constructed models were subjected for Ramachandran plot analysis to validate the quality of the structures. A total of 69 structures were considered to be of significant quality and were submitted to the online database PMDB. Conclusion: These predicted structures would help greatly in identification and drug design to various strains of M. tuberculosis that are sensitive and resistant to different antibiotics. This would greatly help in drug development and personalized drug treatment against different strains of the pathogen. This database would significantly support the structure-based computational drug design applications toward personalized medicine in regard to differences in the various strains of the pathogen.

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