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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Ligand Binding Sites02:40

Ligand Binding Sites

Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...

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Related Experiment Video

Updated: Jun 27, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs.

Arlo Randall1, Pierre Baldi

  • 1School of Information and Computer Sciences, University of California, Irvine, CA 92697, USA. arandall@ics.uci.edu

BMC Structural Biology
|December 6, 2008
PubMed
Summary
This summary is machine-generated.

SELECTpro is a new structure-based method for selecting accurate protein models. It uses predicted structural features to identify the most native-like protein structure, outperforming other methods in CASP7 and on benchmark datasets.

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Last Updated: Jun 27, 2026

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Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • Protein tertiary structure prediction is crucial in computational biology.
  • Selecting the most native-like model from predictions is a key challenge.
  • Structure-based methods offer advantages over consensus methods for model selection.

Purpose of the Study:

  • To develop a structure-based model selection method.
  • The method should utilize predicted structural features.
  • It must be applicable to any set of predicted protein models.

Main Methods:

  • Developed SELECTpro, a novel structure-based model selection method.
  • Incorporated physical, statistical, and predicted structural terms in an energy function.
  • Included novel terms: predicted secondary structure, solvent accessibility, contact map, beta-strand pairing, and side-chain hydrogen bonding.

Main Results:

  • SELECTpro achieved top results in the CASP7 model quality assessment category.
  • The average GDT-TS difference between SELECTpro's top model and the native model was 5.07.
  • SELECTpro outperformed the I-TASSER method on a benchmark set of small proteins with large decoy sets.

Conclusions:

  • SELECTpro is an effective and versatile model selection method.
  • It is suitable for any model set, regardless of size or redundancy.
  • SELECTpro is available as a standalone application and public server.