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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.
Newman Projections02:06

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as conformers.
Determination of Crystal Structures01:29

Determination of Crystal Structures

In the late 1800s, the revelation that light extended beyond visible wavelengths led to the discovery of X-rays by Wilhelm Roentgen. Recognized as high-energy electromagnetic radiation with short wavelengths, X-rays prompted exploration into their interaction with crystals. Max von Laue proposed in 1912 that the periodic arrangement of atoms, ions, or molecules in crystals would cause them to diffract X-rays, a hypothesis confirmed through experiments with copper sulfate and zinc sulfide...
VSEPR Theory02:37

VSEPR Theory

Valence shell electron-pair repulsion theory (VSEPR theory) enables us to predict the molecular structure around a central atom from an examination of the number of bonds and lone electron pairs in its Lewis structure. The VSEPR model assumes that electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between these electron pairs by maximizing the distance between them. The electrons in the valence shell of a central atom form either bonding...
Structures of Solids02:22

Structures of Solids

Solids in which the atoms, ions, or molecules are arranged in a definite repeating pattern are known as crystalline solids. Metals and ionic compounds typically form ordered, crystalline solids. A crystalline solid has a precise melting temperature because each atom or molecule of the same type is held in place with the same forces or energy. Amorphous solids or non-crystalline solids (or, sometimes, glasses) which lack an ordered internal structure and are randomly arranged. Substances that...

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Related Experiment Video

Updated: Jun 28, 2026

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
14:44

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Published on: December 16, 2013

A knowledge-based structure-discriminating function that requires only main-chain atom coordinates.

Yoshihide Makino1, Nobuya Itoh

  • 1Department of Biotechnology, Faculty of Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu-shi, Toyama 939-0398, Japan. makino@pu-toyama.ac.jp

BMC Structural Biology
|October 30, 2008
PubMed
Summary
This summary is machine-generated.

We developed a new knowledge-based pseudo-energy function, DFMAC, for protein structure evaluation. This method effectively identifies near-native protein structures using only main-chain atom coordinates, improving protein structure prediction.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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A Protocol for Computer-Based Protein Structure and Function Prediction

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Related Experiment Videos

Last Updated: Jun 28, 2026

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR
14:44

Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

Published on: December 16, 2013

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Science

Background:

  • Knowledge-based potential functions are crucial for evaluating protein structures.
  • Assessing discrimination ability using decoy structures is a common performance metric.
  • Coarse-grained structure evaluation offers advantages but often sacrifices performance.

Purpose of the Study:

  • To develop a knowledge-based pseudo-energy function for protein structure discrimination.
  • To create a function that utilizes simplified structural representations for efficiency.

Main Methods:

  • Developed the Discriminating Function using Main-chain Atom Coordinates (DFMAC).
  • DFMAC incorporates six pseudo-energy components analyzing different structural features.
  • Input requires only main-chain atom coordinates (N, Cα, C) of residues.

Main Results:

  • DFMAC successfully identified 76.6% of native and 88.3% of near-native (< 2.0 Å Cα RMSD) targets.
  • The function achieved an average Cα RMSD of 1.174 on the test set.
  • Orientation-dependent components significantly contributed to the discrimination performance.

Conclusions:

  • DFMAC demonstrates significant structure discrimination ability despite reduced input representation.
  • The function is suitable for identifying near-native structures in protein structure prediction studies.