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Updated: Oct 11, 2025

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Paratope states in solution improve structure prediction and docking.

Monica L Fernández-Quintero1, Anna Vangone2, Johannes R Loeffler1

  • 1Department of General, Inorganic and Theoretical Chemistry, and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.

Structure (London, England : 1993)
|November 28, 2021
PubMed
Summary
This summary is machine-generated.

Accurately predicting antibody-antigen interactions is challenging. This study reveals that considering antibody paratope states in solution, not just static structures, significantly improves docking and structure prediction for difficult cases.

Keywords:
antibody engineeringantibody structure predictionantibody-antigen dockingantibody-antigen recognitioninterface dynamicsparatope states in solutionprotein-protein docking benchmark

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A Protocol for Computer-Based Protein Structure and Function Prediction
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Area of Science:

  • Computational biology
  • Structural biology
  • Biophysics

Background:

  • Accurate prediction of antibody-antigen interactions is crucial for therapeutic antibody development.
  • Static X-ray structures often fail to capture the dynamic nature of antibody recognition.
  • Conformational changes in antibodies upon antigen binding present significant challenges for computational modeling.

Purpose of the Study:

  • To investigate the role of antibody conformational dynamics in antigen recognition.
  • To explore the utility of paratope states in improving antibody-antigen docking.
  • To analyze the thermodynamics and kinetics of antibody conformational rearrangements.

Main Methods:

  • Utilizing molecular dynamics (MD) simulations starting from unbound antibody X-ray structures.
  • Analyzing conformational changes and paratope states during antigen binding.
  • Investigating thermodynamics and transition kinetics of antibody rearrangements.

Main Results:

  • A single static antibody X-ray structure is insufficient for predicting antigen recognition.
  • Molecular dynamics simulations reveal binding-competent conformations distinct from unbound structures.
  • Kinetically dominant paratope conformations are preferentially selected by complementary antigen conformations.

Conclusions:

  • Antibody paratope states in solution are critical for accurate antibody-antigen docking.
  • Incorporating conformational dynamics improves structure prediction for challenging antibody-antigen systems.
  • This approach enhances the reliability of computational methods in antibody design.