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

You might also read

Related Articles

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

Sort by

Same author

Will there ever be an in vitro assay that is predictive for human hepatotoxicity?

Archives of toxicology·2026

Same author

Update of the Methyltransferase Gene Family: Classification, Evolution and Biological Functions.

Human genomics·2026

Same author

Structure-Guided Development of NRAS G12D Inhibitors Based on a 5‑Azaindole Core.

ACS medicinal chemistry letters·2026

Same author

Olive tree at the intersection of environment, public health, and One Health: a sustainable path to global wellbeing.

Frontiers in public health·2025

Same author

Poziotinib for EGFR exon 20-insertion NSCLC: Clinical efficacy of the phase 2 ZENITH trial and differential impact of EGFR exon 20 insertion location on sensitivity.

Nature communications·2025

Same author

Allosteric targeting of RIPK1: discovery of novel inhibitors <i>via</i> parallel virtual screening and structure-guided optimization.

RSC medicinal chemistry·2025

Same journal

Advancing Biochemical Molecule Registration, Representation and Search for New Drug Modalities.

Journal of chemical information and modeling·2026

Same journal

A Unified Molecular Graph and Protein Language Model Framework for Predicting Human Drug-Hormone Receptor Interactions with Structure-Aware Validation.

Journal of chemical information and modeling·2026

Same journal

Intricate Role of Cholesterol in Membrane Fusion.

Journal of chemical information and modeling·2026

Same journal

tmGNN-XAI: An Explainable Graph Neural Network Tool for Predicting Electronic Properties of Transition Metal Complexes from SMILES.

Journal of chemical information and modeling·2026

Same journal

QSAR in the Browser: An Interactive Cheminformatics Web Application.

Journal of chemical information and modeling·2026

Same journal

FoldDoF: Utilizing the Primary Degrees of Freedom of Protein Backbone for Geometric Modeling and Generation.

Journal of chemical information and modeling·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Nov 21, 2025

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Published on: March 22, 2019

GARD: a Generally Applicable Replacement for RMSD.

J Christian Baber¹, David C Thompson, Jason B Cross

¹Chemical Sciences, Wyeth Research, Cambridge, MA 02140, USA. baberj@wyeth.com

Journal of Chemical Information and Modeling

|July 22, 2009

Summary

This summary is machine-generated.

A new method, Generally Applicable Replacement for rmsD (GARD), offers a chemically aware and normalized alternative to root-mean-squared deviation (rmsd). GARD overcomes rmsd

More Related Videos

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Published on: October 21, 2018

Related Experiment Videos

Last Updated: Nov 21, 2025

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

Published on: March 22, 2019

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Structural Studies of Macromolecules in Solution using Small Angle X-Ray Scattering

Published on: November 5, 2018

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling

Published on: October 21, 2018

Area of Science:

Computational chemistry
Structural bioinformatics
Drug discovery

Background:

Root-mean-squared deviation (rmsd) is a standard metric for comparing molecular structures.
Traditional rmsd has limitations: difficult interpretation, unweighted atomic contributions, and lack of normalization.
These limitations impact its reliability in assessing molecular docking and conformational analysis.

Purpose of the Study:

Introduce a novel, chemically aware metric: Generally Applicable Replacement for rmsD (GARD).
Address the shortcomings of traditional rmsd.
Provide a more robust and interpretable measure for comparing chemical structures.

Main Methods:

Developed GARD, a novel distance metric for aligned chemical structures.
Incorporated atomic weighting based on statistical binding importance (Andrews et al.).
Ensured GARD is normalized and chemically aware.

Main Results:

GARD demonstrates improved interpretability and chemical relevance compared to rmsd.
The method effectively assesses molecular docking software performance.
GARD successfully identifies and corrects for high rmsd in otherwise accurate molecular poses.

Conclusions:

GARD offers a superior alternative to rmsd for evaluating molecular structures.
Its chemical awareness and normalization make it suitable for docking pose assessment and conformer comparison.
GARD enhances the reliability of structural comparisons in computational chemistry.