Homology modeling using SWISS-Model for Biochemistry I v1

2021 ◽  
Author(s):  
Michael Friedman ◽  
Chris Berndsen
Keyword(s):  
Nucleic Acids ◽  
Homology Modeling ◽  
Homology Modelling ◽  
Protein Structures ◽  
Web Server ◽  
James Madison

Protocol for homology modeling proteins for use in Biochemistry I at James Madison University. Protocol guides students to use the SWISS-Model web server (citations below). Citations for servers: Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R., and Schwede, T. (2018) SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46, W296–W303.

Protein modeling by homology using the example of tick-borne encephalitis serine protease NS3

2020 ◽  
pp. 59-66
Author(s):  
Nikita Ilment ◽  
Ekaterina Zinina
Keyword(s):  
Electron Microscopy ◽  
Homology Modeling ◽  
Homology Modelling ◽  
Protein Structures ◽  
3D Structure ◽  
Free Software ◽  
Homologous Proteins ◽  
Cryo Electron Microscopy ◽  
Tick Borne Encephalitis ◽  
Sequences Analysis

Homology modeling is a process of obtaining a 3D structure of a protein using various algorithms based on already known structures of homologous proteins. The spatial structure of protein is required for in silico protein evaluation. 3D structures can be obtained using different methods: NMR, Xray crystallography (XRC), and cryo-electron microscopy (cryo-EM), but these methods require a lot of time and money. At the same time, the speed of nucleotide sequences analysis is increasing, thereby creating a mismatch between the number of decoded genomes and the investigated 3D protein structures that are encoded by these sequences. Also, homology modeling is the easiest and fastest way to obtain the model of the desired protein. This review describes free software for homology modelling — SWISS-MODEL and MODELLER, how to use it and how to evaluate the results.

scholarly journals 3D-PP: A Tool for Discovering Conserved Three-Dimensional Protein Patterns

2019 ◽  
Vol 20 (13) ◽  
pp. 3174
Author(s):  
Alejandro Valdés-Jiménez ◽  
Josep-L. Larriba-Pey ◽  
Gabriel Núñez-Vivanco ◽  
Miguel Reyes-Parada
Keyword(s):  
Homology Modeling ◽  
In Silico ◽  
Rational Design ◽  
Protein Structures ◽  
Three Dimensional ◽  
Web Server ◽  
Free Access ◽  
Protein Patterns ◽  
Structural Motifs ◽  
The Web

Discovering conserved three-dimensional (3D) patterns among protein structures may provide valuable insights into protein classification, functional annotations or the rational design of multi-target drugs. Thus, several computational tools have been developed to discover and compare protein 3D-patterns. However, most of them only consider previously known 3D-patterns such as orthosteric binding sites or structural motifs. This fact makes necessary the development of new methods for the identification of all possible 3D-patterns that exist in protein structures (allosteric sites, enzyme-cofactor interaction motifs, among others). In this work, we present 3D-PP, a new free access web server for the discovery and recognition all similar 3D amino acid patterns among a set of proteins structures (independent of their sequence similarity). This new tool does not require any previous structural knowledge about ligands, and all data are organized in a high-performance graph database. The input can be a text file with the PDB access codes or a zip file of PDB coordinates regardless of the origin of the structural data: X-ray crystallographic experiments or in silico homology modeling. The results are presented as lists of sequence patterns that can be further analyzed within the web page. We tested the accuracy and suitability of 3D-PP using two sets of proteins coming from the Protein Data Bank: (a) Zinc finger containing and (b) Serotonin target proteins. We also evaluated its usefulness for the discovering of new 3D-patterns, using a set of protein structures coming from in silico homology modeling methodologies, all of which are overexpressed in different types of cancer. Results indicate that 3D-PP is a reliable, flexible and friendly-user tool to identify conserved structural motifs, which could be relevant to improve the knowledge about protein function or classification. The web server can be freely utilized at https://appsbio.utalca.cl/3d-pp/.

scholarly journals DaReUS-Loop: a web server to model multiple loops in homology models

2019 ◽  
Vol 47 (W1) ◽  
pp. W423-W428 ◽  
Author(s):  
Yasaman Karami ◽  
Julien Rey ◽  
Guillaume Postic ◽  
Samuel Murail ◽  
Pierre Tufféry ◽  
...  
Keyword(s):  
Homology Modeling ◽  
Open Problem ◽  
Protein Structures ◽  
Web Server ◽  
Graphical Interface ◽  
Loop Modeling ◽  
Prediction Confidence ◽  
Loop Regions ◽  
Automated Platform ◽  
Homology Models

AbstractLoop regions in protein structures often have crucial roles, and they are much more variable in sequence and structure than other regions. In homology modeling, this leads to larger deviations from the homologous templates, and loop modeling of homology models remains an open problem. To address this issue, we have previously developed the DaReUS-Loop protocol, leading to significant improvement over existing methods. Here, a DaReUS-Loop web server is presented, providing an automated platform for modeling or remodeling loops in the context of homology models. This is the first web server accepting a protein with up to 20 loop regions, and modeling them all in parallel. It also provides a prediction confidence level that corresponds to the expected accuracy of the loops. DaReUS-Loop facilitates the analysis of the results through its interactive graphical interface and is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/DaReUS-Loop/.

The visualCMAT: A web-server to select and interpret correlated mutations/co-evolving residues in protein families

2018 ◽  
Vol 16 (02) ◽  
pp. 1840005 ◽  
Author(s):  
Dmitry Suplatov ◽  
Yana Sharapova ◽  
Daria Timonina ◽  
Kirill Kopylov ◽  
Vytas Švedas
Keyword(s):  
Rational Design ◽  
Visual Analysis ◽  
Structural Information ◽  
Protein Structures ◽  
Web Server ◽  
Physical Contact ◽  
Protein Families ◽  
Sequence Alignments ◽  
Homologous Proteins ◽  
Correlated Mutations

The visualCMAT web-server was designed to assist experimental research in the fields of protein/enzyme biochemistry, protein engineering, and drug discovery by providing an intuitive and easy-to-use interface to the analysis of correlated mutations/co-evolving residues. Sequence and structural information describing homologous proteins are used to predict correlated substitutions by the Mutual information-based CMAT approach, classify them into spatially close co-evolving pairs, which either form a direct physical contact or interact with the same ligand (e.g. a substrate or a crystallographic water molecule), and long-range correlations, annotate and rank binding sites on the protein surface by the presence of statistically significant co-evolving positions. The results of the visualCMAT are organized for a convenient visual analysis and can be downloaded to a local computer as a content-rich all-in-one PyMol session file with multiple layers of annotation corresponding to bioinformatic, statistical and structural analyses of the predicted co-evolution, or further studied online using the built-in interactive analysis tools. The online interactivity is implemented in HTML5 and therefore neither plugins nor Java are required. The visualCMAT web-server is integrated with the Mustguseal web-server capable of constructing large structure-guided sequence alignments of protein families and superfamilies using all available information about their structures and sequences in public databases. The visualCMAT web-server can be used to understand the relationship between structure and function in proteins, implemented at selecting hotspots and compensatory mutations for rational design and directed evolution experiments to produce novel enzymes with improved properties, and employed at studying the mechanism of selective ligand’s binding and allosteric communication between topologically independent sites in protein structures. The web-server is freely available at https://biokinet.belozersky.msu.ru/visualcmat and there are no login requirements.

scholarly journals SWISS-MODEL: homology modelling of protein structures and complexes

2018 ◽  
Vol 46 (W1) ◽  
pp. W296-W303 ◽  
Author(s):  
Andrew Waterhouse ◽  
Martino Bertoni ◽  
Stefan Bienert ◽  
Gabriel Studer ◽  
Gerardo Tauriello ◽  
...  
Keyword(s):  
Homology Modelling ◽  
Protein Structures

A Basic Molecular Analysis of the Diabetic Antigen GAD by Homology Modelling. Principles of the Method and Understanding of Antigenicity and Binding Sites

Pteridines ◽  
2007 ◽  
Vol 18 (1) ◽  
pp. 79-94
Author(s):  
Marco Wiltgen ◽  
Gernot P. Tilz
Keyword(s):  
Active Site ◽  
Protein Sequence ◽  
Structure Prediction ◽  
Structural Information ◽  
Homology Modelling ◽  
Protein Structures ◽  
Dopa Decarboxylase ◽  
Gad 65 ◽  
Unknown Structure ◽  
Introductory Paper

Abstract Functional specificity of a protein is linked to its structure. A growing section of bioinformatics deals with the prediction and visualization of protein 3D structures. In homology modelling, a protein sequence with an unknown structure is aligned with sequences of known protein structures. By exploiting structural information from the known configurations, the new structure can be predicted. In this introductory paper, we will present the principles of homology modelling and demonstrate the method used, by determining the structure of the enzyme glutamic decarboxylase (GAD 65). This protein is an autoantigen involved in several human autoimmune diseases. We will illustrate the different steps in structure prediction of GAD 65 by use of two experimentally determined structures of pig kidney DOPA decarboxylase (one structure in complex with the inhibitor carbidopa) as templates. The resulting model of GAD 65 provides detailed information about the active site of the protein and selected epitopes. By analysis of the interactions between the DOPA decarboxylase with the inhibitor carbidopa, the residues of the GAD 65 active site can be identified via the sequence alignment between DOPA and GAD 65. The locations of known epitopes in the molecule are visualized in special representations giving insights into mechanisms of antigenicity. Hydrophobicity analysis gives first hints for the adherence ability of GAD 65 to the cell membrane. Homology modelling is at present one of the most efficient techniques to provide accurate structural models of proteins. It is expected that in few years, for every new determined protein sequence, at least one member with a known structure of the same protein family will be available, which will steadily increase the importance and applicability of homology modelling.

A solution-free crystal-mounting platform for native SAD

2020 ◽  
Vol 76 (10) ◽  
pp. 938-945
Author(s):  
Jian Yu ◽  
Akira Shinoda ◽  
Koji Kato ◽  
Isao Tanaka ◽  
Min Yao
Keyword(s):  
Data Collection ◽  
Nucleic Acids ◽  
Protein Structures ◽  
Anomalous Scattering ◽  
X Rays ◽  
Long Wavelength ◽  
Light Atoms ◽  
Sad Phasing ◽  
Anomalous Signal

The native SAD phasing method uses the anomalous scattering signals from the S atoms contained in most proteins, the P atoms in nucleic acids or other light atoms derived from the solution used for crystallization. These signals are very weak and careful data collection is required, which makes this method very difficult. One way to enhance the anomalous signal is to use long-wavelength X-rays; however, these wavelengths are more strongly absorbed by the materials in the pathway. Therefore, a crystal-mounting platform for native SAD data collection that removes solution around the crystals has been developed. This platform includes a novel solution-free mounting tool and an automatic robot, which extracts the surrounding solution, flash-cools the crystal and inserts the loop into a UniPuck cassette for use in the synchrotron. Eight protein structures (including two new structures) have been successfully solved by the native SAD method from crystals prepared using this platform.

scholarly journals Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling

2011 ◽  
Vol 27 (18) ◽  
pp. 2537-2545 ◽  
Author(s):  
Sheng Wang ◽  
Jian Peng ◽  
Jinbo Xu
Keyword(s):  
Homology Modeling ◽  
Protein Structures ◽  
Related Protein

scholarly journals Editorial: Nucleic Acids Research annual Web Server Issue in 2014

2014 ◽  
Vol 42 (W1) ◽  
pp. W1-W2 ◽  
Author(s):  
Gary Benson
Keyword(s):  
Nucleic Acids ◽  
Web Server
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