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SERF: a program for accessible surface area calculations

D R Flower1

  • 1Department of Physical and Metabolic Sciences, Astra Charnwood, Loughborough, Leicestershire, UK.

Journal of Molecular Graphics & Modelling
|August 1, 1997
PubMed
Summary
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The SERF program enhances accessible surface area calculations for protein structure analysis. It offers multiple methods to study surface area changes during binding and complexation.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Biochemistry

Background:

  • Accessible surface area (ASA) calculations are crucial for understanding protein structure and function.
  • Current methods may have limitations in accuracy or computational efficiency.
  • Analyzing ASA changes upon binding and complexation provides insights into molecular interactions.

Purpose of the Study:

  • To introduce the SERF program, designed to facilitate ASA calculations in protein structure analysis.
  • To provide a tool for analyzing ASA changes during protein binding and complexation.
  • To compare different ASA calculation methodologies.

Main Methods:

  • Implementation of multiple algorithms for ASA calculation within the SERF program.
  • Inclusion of methods that approximate residues using single spheres for simplified analysis.

Related Experiment Videos

  • Discussion of algorithmic details and comparative performance of implemented methods.

    • Main Results:

    • The SERF program offers a flexible platform for diverse ASA calculations.
    • Comparative analysis demonstrates the performance of different implemented methods.
    • The software implementation facilitates practical application in structural biology.

    Conclusions:

    • SERF enhances the utility of ASA calculations in protein structure analysis.
    • The program supports the investigation of molecular interactions through surface area change analysis.
    • SERF provides a valuable tool for researchers in structural biology and computational chemistry.