Calculation of protein conformation by global optimization of a potential energy function

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Updated: Oct 18, 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

J Lee1, A Liwo, D R Ripoll

  • 1Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.

Proteins
|October 20, 1999
PubMed

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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.
Protein Organization01:28

Protein Organization

Proteins are one of the fundamental building blocks of life that carry out many diverse functions in the cell. Proteins are assembled from amino acids. The sequence of amino acids is known as the primary structure of a protein. Local interactions of individual amino acids cause the linear chain to fold into the secondary structures. Interactions of distant amino acids lead to further folding of the protein—the tertiary structure. The assembly of multiple folded chains (subunits) is known as...
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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
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Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation which is critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.Protein Structure Is Critical to Its Biological FunctionProteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
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Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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