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GapRepairer: a server to model a structural gap and validate it using topological analysis.

Aleksandra I Jarmolinska1,2, Michal Kadlof1,3, Pawel Dabrowski-Tumanski1,4

  • 1Centre of New Technologies, University of Warsaw, Warsaw, Poland.

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|May 3, 2018
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Summary
This summary is machine-generated.

GapRepairer is a new web server that models protein structures with correct topology. It helps users, even non-experts, to build accurate protein models by considering knots and links for improved function.

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Area of Science:

  • Biophysics
  • Biotechnology
  • Molecular Biology

Background:

  • Protein structures often have unresolved fragments (over 25%) and non-trivial topologies like knots and links (approx. 6%).
  • Protein topology is crucial for function, yet current modeling tools neglect it, requiring specialized expertise.

Purpose of the Study:

  • To introduce GapRepairer, a novel web server for protein structure modeling.
  • To address the gap in modeling methods by incorporating protein topology considerations.
  • To provide an accessible tool for generating topologically correct protein models.

Main Methods:

  • GapRepairer utilizes Modeller homology modeling.
  • The server determines the topology of both template and predicted protein structures.
  • It offers an intuitive interface for non-expert users.

Main Results:

  • GapRepairer successfully models protein structures, accounting for topology.
  • The server provides topology information to guide model selection or design.
  • It enables users to score models or design artificial (dis)entangled structures.

Conclusions:

  • GapRepairer enhances protein structure modeling by integrating topological information.
  • The server democratizes access to advanced protein modeling techniques.
  • It supports research in biophysics, biotechnology, and molecular biology by enabling the creation of functionally relevant protein structures.