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Molecular Models

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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.

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Updated: Jul 1, 2025

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

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Published on: July 25, 2013

Generalized biomolecular modeling and design with RoseTTAFold All-Atom.

Rohith Krishna^1,2, Jue Wang^1,2, Woody Ahern^1,2,3

¹Department of Biochemistry, University of Washington, Seattle, WA 98105, USA.

Science (New York, N.Y.)

|March 7, 2024

Summary

RoseTTAFold All-Atom models complex biological assemblies, including proteins, nucleic acids, and small molecules. This new deep learning approach enables the design of novel proteins that bind specific small molecules.

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Published on: December 25, 2021

Area of Science:

Computational biology
Structural biology
Biochemistry

Background:

Deep learning has advanced protein structure prediction but is limited to protein-only systems.
Modeling complex biological assemblies requires integrating diverse chemical entities.

Purpose of the Study:

To develop a deep learning framework capable of modeling and designing complex biological assemblies beyond proteins.
To create a versatile tool for designing proteins that interact with non-protein components.

Main Methods:

Introduced RoseTTAFold All-Atom (RFAA) using a hybrid residue- and atomic-level representation.
Developed RFdiffusion All-Atom (RFdiffusionAA) by fine-tuning on denoising tasks for targeted design.
Utilized crystallography and binding assays for experimental validation.

Main Results:

RFAA successfully models assemblies of proteins, nucleic acids, small molecules, metals, and covalent modifications.
RFdiffusionAA designed de novo proteins that bind specific small molecules.
Validated designs include proteins binding digoxigenin, heme, and bilin.

Conclusions:

RoseTTAFold All-Atom and RFdiffusion All-Atom represent a significant advancement in modeling and designing complex molecular assemblies.
This approach opens new avenues for engineering proteins with desired functions and interactions.