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Related Concept Videos

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.
Molecular Models02:00

Molecular Models

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
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...
Noncovalent Attractions in Biomolecules02:35

Noncovalent Attractions in Biomolecules

Noncovalent attractions are associations within and between molecules that influence the shape and structural stability of complexes. These interactions differ from covalent bonding in that they do not involve sharing of electrons.
Four types of noncovalent interactions are hydrogen bonds, van der Waals forces, ionic bonds, and hydrophobic interactions.
Hydrogen bonding results from the electrostatic attraction of a hydrogen atom covalently bonded to a strong-electronegative atom like oxygen,...
Gene Families01:57

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...

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Related Experiment Video

Updated: May 30, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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

Published on: July 16, 2017

PubChem3D: Biologically relevant 3-D similarity.

Sunghwan Kim1, Evan E Bolton, Stephen H Bryant

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894, USA. bolton@ncbi.nlm.nih.gov.

Journal of Cheminformatics
|July 26, 2011
PubMed
Summary

This study analyzed 3-D similarity scores for millions of compounds, finding that while some assays show separation between active and inactive compounds, it

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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

Related Experiment Videos

Last Updated: May 30, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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

Published on: July 16, 2017

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

Area of Science:

  • Computational chemistry and cheminformatics
  • Drug discovery and development
  • Bioinformatics and computational biology

Background:

  • 3-D similarity techniques are widely used in virtual screening and biological data analysis.
  • A key challenge is defining a biologically meaningful 3-D similarity value.
  • The statistical significance of separating active/active from active/inactive compound spaces remains an open question.

Purpose of the Study:

  • To determine a biologically meaningful 3-D similarity score.
  • To investigate the statistical separation between active/active and active/inactive compound spaces in biological assays.
  • To establish a statistical framework for analyzing 3-D similarity in PubChem data.

Main Methods:

  • Analysis of 269.7 billion unique conformer pairs from 734,486 biologically tested compounds.
  • Calculation of average and standard deviations for six different 3-D similarity measures (STST-opt, CTST-opt, ComboTST-opt, STCT-opt, CTCT-opt, ComboTCT-opt).
  • Examination of 1,389 biological assays to compare 3-D similarity score differences between noninactive-noninactive (NN) and noninactive-inactive (NI) pairs.

Main Results:

  • The study calculated average and standard deviations for six 3-D similarity measures, providing baseline distributions.
  • A trend of separation between NN (active/active) and NI (active/inactive) pairs was observed across assays, but was not always statistically unambiguous.
  • Combo Tanimoto (ComboT) emerged as the most efficient score type for identifying cases with clear separation.

Conclusions:

  • A statistical guideline for analyzing biological assay data using 3-D similarity and PubChem tools was established.
  • Using a single conformer per compound, a limited number of assays demonstrated clear separation between active/active and active/inactive spaces.
  • Further research with multiple conformers per compound may refine these findings.