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Related Experiment Video

Updated: Jan 4, 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

Protein Structural Information and Evolutionary Landscape by In Vitro Evolution.

Marco Fantini¹, Simonetta Lisi¹, Paolo De Los Rios^2,3

¹BioSNS Laboratory of Biology, Scuola Normale Superiore (SNS), Pisa, Italy.

Molecular Biology and Evolution

|November 1, 2019

Summary

This summary is machine-generated.

Researchers developed a new method to study protein structure and evolution by selecting for protein function. This approach, Coupling Analysis by Molecular Evolution Library Sequencing (CAMELS), reveals evolutionary landscapes without needing purified proteins or physical measurements.

Keywords:

AmpR DCA PacBio SMRT sequencing Sequel beta-lactamase direct coupling analysis error-prone PCR evolutionary couplings molecular evolution mutagenesis third-generation sequencing β-lactamase

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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:

Structural biology
Evolutionary biology
Biochemistry

Background:

Protein structure and function are intrinsically linked through evolution.
Understanding this relationship is a central goal of structural biology.
Existing methods often require purified proteins or physical measurements.

Purpose of the Study:

To investigate if protein function can be used to infer structure and evolutionary history.
To develop a novel methodology for in vitro protein evolution driven by functional selection.

Main Methods:

Developed Coupling Analysis by Molecular Evolution Library Sequencing (CAMELS).
Applied CAMELS to study TEM-1 beta-lactamase.
Generated and sequenced large libraries of mutational variants under functional selection.

Main Results:

CAMELS successfully revealed local fold features of TEM-1 beta-lactamase.
The method elucidated aspects of the protein's structural and evolutionary landscape.
Demonstrated the ability to map landscapes using functional selection alone.

Conclusions:

Functional selection can be exploited to gain insights into protein structure and early evolutionary paths.
CAMELS offers a powerful alternative to traditional methods, bypassing the need for purified proteins or physical data.
This approach opens new avenues for studying protein evolution and structure-