Protein Folding Software

  • Richard Dods


This chapter (Protein folding software) presents large pools of folded structures as determined by X-ray diffraction crystallography. The amino acid sequences for which three-dimensional structure has been ascertained are used to align the amino acid sequences in other proteins and determine their three-dimensional structures. The known structures are compiled in protein libraries such as the Proton Data Bank (PDB) and SWISS-PROT database. BLAST is a computer program that searches the data bank of proteins that have known structure and aligns the amino acid sequences in similar proteins. The efficacy of programs that determine the structure from known structures are assessed by CASP. The above type of analysis is called homology modeling. Protein threading is also described in this chapter. Ab initio modeling is used when there are few or no proteins for the comparison of protein structures. Transition state theory, similar to the transition state as used in organic/inorganic chemistry, is explained. Molecular dynamics, a powerful tool used for the investigation of protein folding, is described. Also Monte Carlo Simulations and Markov State Models are discussed in this chapter. We further explore amino acids and their involvement in α-helical and β-pleated sheets. Β-barrel proteins using hyperboloid computer programs are described. Other computer programs such as QUARK, I-TASSER, Modeller, Amber, and the Hidden Markov Model are also explained.



Ab initio modeling

predicts the folding of a protein from scratch (or a low NEFF)


are amino acid pairs that are a least 8 Å apart.

Critical assessment of protein structure prediction (CASP)

program assesses a new procedure for the determination of the folding of a protein.


refers to a molecule binding to a protein


includes helices, helical bundles, β-pleated sheets, and β-pleated barrel structures.

Hidden Markov model

contains a Markov chain in which the state of the system is only partially observable.

Homology Modeling

is the alignment of an amino acid sequence with a known three-dimensional structure (template) with a protein of unknown structure (target) protein.

Hyperboloid of revolution

is a surface generated by rotating a hyperbola around the principal axes of the surface.

Markov chain

describes a sequence of events in which the probability of each event is dependent on the previous history of that event.

Markov Property

is a random process where the future state of the process is not dependent on the previous state of the process.

Molecular dynamics

is a computer simulation method for the study of the movement of proteins during a fixed time.

Monte Carlo simulation (MC)

is a random probability that is calculated to give a number that is characterized by its standard deviation. For example, 20 ± 2 means that the mean for this parameter is 20 but could range from 18 to 22. There is no single MC methodology.

Protein threading

is a modelling procedure for proteins that have the same folding as proteins that have had their three dimensional structures determined by X-ray diffraction or NMR.

Shear number (S)

is determined by the number of amino acids that do not align themselves when the crease in the β-barrel produced by the first polypeptide chain and the last polypeptide chain align themselves side by side.

The HH-suite software package

includes HHpred a server for protein homologous detection and structure prediction. HHpred is based on HHsearch and HHblits.

The position-specific iterative basic local alignment search tool (PSI-BLAST)

detects distant phylogenetic relationships among proteins.


are defined as the regular arrangement of β-pleated chains surrounding a central pore.

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Richard Dods
    • 1
  1. 1.Illinois Mathematics and Science AcademyPalatineUSA

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