Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Protein Organization

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.

Conserved Binding Sites

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Toward a Random Background for Ligand Optimization.

bioRxiv : the preprint server for biology·2026

Same author

A functional investigation of antibody Fc-FcRn variant binding guided by <i>in silico</i> free energy perturbation methods.

bioRxiv : the preprint server for biology·2026

Same author

Results of a Large-Scale Study of the Binding of 50 Type II Inhibitors to 348 Kinases: The Role of Protein Reorganization.

Journal of medicinal chemistry·2026

Same author

Evaluating Multiconfigurational Trials for Accurate Phaseless Auxiliary-Field Quantum Monte Carlo on 3d Transition Metal Complexes.

Journal of chemical theory and computation·2026

Same author

An Accurate Charge-Aware Machine-Learning Interatomic Potential for the Reduction of Li-Ion Battery Electrolytes in Solution.

Journal of chemical theory and computation·2026

Same author

Results of a large scale study of the binding of 50 type II inhibitors to 348 kinases: The role of protein reorganization.

bioRxiv : the preprint server for biology·2026

Search research articles

Related Experiment Video

Updated: May 11, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

Computational methods for high resolution prediction and refinement of protein structures.

Richard A Friesner¹, Robert Abel, Dahlia A Goldfeld

¹Department of Chemistry, Columbia University, New York, NY, USa. rich@chem.columbia.edu

Current Opinion in Structural Biology

|May 22, 2013

Summary

Advances in implicit solvation and sampling algorithms improve prediction of localized protein structures. New methods achieve sub-angstrom accuracy for large loops, offering potential for homology modeling refinement.

More Related Videos

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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

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

Published on: July 25, 2013

Related Experiment Videos

Last Updated: May 11, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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

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

Published on: July 25, 2013

Area of Science:

Computational Biology
Structural Biology
Biophysics

Background:

Predicting and refining localized protein structures, such as loops, is crucial for understanding protein function.
Existing methods face challenges in accurately modeling complex local conformations and energetics.

Purpose of the Study:

To review and highlight recent advancements in implicit solvation and sampling algorithms.
To demonstrate enhanced capabilities in predicting and refining localized protein structures to high resolution.

Main Methods:

Improvements to the generalized Born model and hydrophobicity term for more accurate energetics.
Specialized sampling algorithms for reliable prediction of complex local structures (e.g., loop-helix-loop).
Introduction of a novel penalty term for loop dihedral patterns uncommon in experimental structures.

Main Results:

Demonstrated prediction of diverse sets of large loops in their native backbone environment.
Achieved sub-angstrom accuracy in predicting these localized protein structures.
Validated the accuracy of improved generalized Born and hydrophobicity models.

Conclusions:

The reviewed methodology significantly enhances the prediction and refinement of localized protein structures.
The approach shows promise for addressing refinement challenges in homology modeling.
Further development is needed to handle delocalized errors in homology modeling structures.