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

Search research articles

Related Experiment Videos

A database of macromolecular motions

M Gerstein¹, W Krebs

¹Department of Molecular Biophysics and Biochemistry, 266 Whitney Avenue, Yale University, PO Box 208114, New Haven, CT 06520, USA. mark.gerstein@yale.edu

Nucleic Acids Research

|September 2, 1998

Summary

This study introduces MolMovDB, a comprehensive database cataloging macromolecular motions, particularly protein movements. It systematically classifies these motions by size and packing, aiding structural biology research.

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

Distinct forebrain regions define a dichotomous astrocytic profile in multiple system atrophy.

Acta neuropathologica communications·2024

Same author

What is bioinformatics? An introduction and overview.

Yearbook of medical informatics·2016

Same author

A Retinal Prosthesis Technology Based on CMOS Microelectronics and Microwire Glass Electrodes.

IEEE transactions on biomedical circuits and systems·2013

Same author

A contribution to crystallographic Carcinoma diagnosis according to E. Pfeiffer.

Helvetica chirurgica acta·2010

Same author

Novel transcribed regions in the human genome.

Cold Spring Harbor symposia on quantitative biology·2007

Same author

The geometry of the ribosomal polypeptide exit tunnel.

Journal of molecular biology·2006

Area of Science:

Structural Biology
Bioinformatics
Computational Biology

Background:

Macromolecular motions are crucial for biological function.
Systematic classification and accessibility of motion data are lacking.
Understanding protein and nucleic acid dynamics requires comprehensive structural information.

Purpose of the Study:

To create a comprehensive, web-accessible database of macromolecular motions.
To systematize instances of protein and nucleic acid movement with structural data.
To provide a standardized framework for describing and analyzing molecular dynamics.

Main Methods:

Development of the Macromolecular Motions Database (MolMovDB).
Hierarchical classification of protein motions based on size (fragment, domain, subunit) and packing (shear, hinge, other).
Incorporation of evidence type (experimental, inferred) and standardized motion nomenclature.

Main Results:

The database currently contains over 120 macromolecular motions, primarily proteins.
A hierarchical classification system for protein motions is established.
The database supports standardized descriptions of motion aspects and evidence.

Conclusions:

MolMovDB provides a valuable resource for the structural biology community.
The database is transitioning to an object-relational model for improved data handling.
It offers tools for visualizing motion pathways and generating movies from coordinates.

Related Experiment Videos