Overcoming sequence misalignments with weighted structural superposition

Fragment Finder 2.0is a web-based interactive computing server which can be used to retrieve structurally similar protein fragments from 25 and 90% nonredundant data sets. The computing server identifies structurally similar fragments using the protein backbone Cα angles. In addition, the identified fragments can be superimposed using either of the two structural superposition programs,STAMPandPROFIT, provided in the server. The freely available Java plug-inJmolhas been interfaced with the server for the visualization of the query and superposed fragments. The server is the updated version of a previously developed search engine and employs an in-house-developed fast pattern matching algorithm. This server can be accessed freely over the World Wide Web through the URL http://cluster.physics.iisc.ernet.in/ff/.

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Comparing programs for rigid‐body multiple structural superposition of proteins

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.20975 ◽

2006 ◽

Vol 64 (1) ◽

pp. 219-226 ◽

Cited By ~ 4

Author(s):

Anthony D. Hill ◽

Peter J. Reilly

Keyword(s):

Rigid Body ◽

Structural Superposition

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Molecular replacement withMOLREP

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444909042589 ◽

2009 ◽

Vol 66 (1) ◽

pp. 22-25 ◽

Cited By ~ 2183

Author(s):

Alexei Vagin ◽

Alexei Teplyakov

Keyword(s):

Rigid Body ◽

Electron Density ◽

Input Data ◽

Molecular Replacement ◽

Data Preparation ◽

X Ray ◽

Search Models ◽

Automatic Mode ◽

Structural Superposition ◽

Fully Automatic

MOLREPis an automated program for molecular replacement that utilizes a number of original approaches to rotational and translational search and data preparation. Since the first publication describing the program,MOLREPhas acquired a variety of features that include weighting of the X-ray data and search models, multi-copy search, fitting the model into electron density, structural superposition of two models and rigid-body refinement. The program can run in a fully automatic mode using optimized parameters calculated from the input data.

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Classification of ligand molecules in PDB with graph match-based structural superposition

Journal of Structural and Functional Genomics ◽

10.1007/s10969-016-9209-x ◽

2016 ◽

Vol 17 (4) ◽

pp. 135-146 ◽

Cited By ~ 1

Author(s):

Clara Shionyu-Mitsuyama ◽

Atsushi Hijikata ◽

Toshiyuki Tsuji ◽

Tsuyoshi Shirai

Keyword(s):

Graph Match ◽

Structural Superposition

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Structural superposition in fault systems bounding Santa Clara Valley, California

Geosphere ◽

10.1130/ges01100.1 ◽

2015 ◽

Vol 11 (1) ◽

pp. 63-75 ◽

Cited By ~ 2

Author(s):

R.W. Graymer ◽

R.G. Stanley ◽

D.A. Ponce ◽

R.C. Jachens ◽

R.W. Simpson ◽

...

Keyword(s):

Fault Systems ◽

Santa Clara Valley ◽

Structural Superposition

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An Approximate Analyt ical (Structural) Superposition in Terms of Two, or More, α - Circuits of the Same Topology: Pt .1 – Description of the Superposition

Journal of Engineering Science and Technology Review ◽

10.25103/jestr.064.05 ◽

2013 ◽

Vol 6 (4) ◽

pp. 33-44

Author(s):

E. Gluskin ◽

Keyword(s):

Structural Superposition

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Sofosbuvir as a potential alternative to treat the SARS-CoV-2 epidemic

10.21203/rs.3.rs-21002/v1 ◽

2020 ◽

Author(s):

Rodrigo Jácome ◽

José Alberto Campillo-Balderas ◽

Samuel Ponce de León ◽

Arturo Becerra ◽

Antonio Lazcano

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Multiple Alignment ◽

Nucleoside Analog ◽

Virus Infections ◽

Structural Superposition ◽

Potential Alternative

Abstract As of today, there is no antiviral for the treatment of the SARS-CoV-2 infection, and the development of a vaccine might take several months or even years. The structural superposition of the hepatitis C virus polymerase bound to sofosbuvir, a nucleoside analog antiviral approved for hepatitis C virus infections, with the SARS-CoV polymerase shows that the residues that bind to the drug are present in the latter. Moreover, a multiple alignment of several SARS-CoV-2, SARS and MERS-related coronaviruses polymerases shows that these residues are conserved in all these viruses, opening the possibility to use sofosbuvir against these highly infectious pathogens.

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