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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

eSPC: an online data-analysis platform for molecular biophysics.

Osvaldo Burastero¹, Stephan Niebling², Lucas A Defelipe²

¹Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2620, Ciudad Autónoma de Buenos Aires, Argentina.

Acta Crystallographica. Section D, Structural Biology

|October 4, 2021

Summary

This study introduces user-friendly online tools for analyzing biophysical data from protein interaction studies. These tools help quantify binding affinities and thermal stability, crucial for understanding cellular mechanisms.

Keywords:

Kd Tm binding affinity differential scanning fluorimetry eSPC ligand screening microscale thermophoresis molecular biophysics molecular interactions online servers open science protein stability

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Last Updated: Jun 14, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

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Published on: November 5, 2018

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Biophysics
Molecular Biology
Biochemistry

Background:

Protein-ligand, protein-peptide, and protein-protein complex formation are fundamental to all biological processes.
Understanding the affinity, kinetics, and thermodynamics of biomolecular interactions is essential for elucidating cellular mechanisms.
Various technologies exist for probing biomolecular interactions, measuring diverse signals like fluorescence, heat, and thermophoresis.

Purpose of the Study:

To present user-friendly online tools for analyzing biophysical data from biomolecular interaction experiments.
To provide accessible methods for quantifying binding affinities and thermal stability parameters.

Main Methods:

Development of an online data-analysis platform (https://spc.embl-hamburg.de/).
Integration of classical thermodynamic models for data fitting.
Application to data from steady-state fluorescence spectroscopy, microscale thermophoresis, and differential scanning fluorimetry.

Main Results:

The platform offers modules for analyzing various biophysical datasets.
User guidelines facilitate the determination of equilibrium dissociation constants (K_d).
The tools enable the calculation of thermal unfolding parameters, including melting temperatures (T_m).

Conclusions:

The developed online tools simplify the analysis of complex biophysical data.
This facilitates the accurate quantification of biomolecular binding and stability.
The platform supports fundamental research in molecular biology and biochemistry.