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Updated: Jun 12, 2026

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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ICM Web: the interactive chromatin modeling web server.

Richard C Stolz1, Thomas C Bishop

  • 1Department of Biostatistics, Tulane University, 1440 Canal Street, Suite 2001, New Orleans, LA 70112, USA.

Nucleic Acids Research
|June 15, 2010
PubMed
Summary
This summary is machine-generated.

The interactive chromatin modeling web server (ICM Web) offers rapid assessment of DNA nucleosome stability and chromatin folding. This tool aids researchers in understanding DNA structure and organization without requiring a login.

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An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

Published on: April 5, 2018

Area of Science:

  • Genomics
  • Computational Biology
  • Biophysics

Background:

  • Understanding DNA structure and its organization into chromatin is crucial for gene regulation.
  • Predicting nucleosome positioning and stability is essential for deciphering genomic functions.
  • Existing tools may lack interactivity or comprehensive modeling capabilities for chromatin folding.

Purpose of the Study:

  • To introduce the interactive chromatin modeling web server (ICM Web) for rapid assessment of nucleosome stability.
  • To provide a user-friendly platform for folding DNA sequences into chromatin templates.
  • To enable interactive investigation of chromatin dynamics and DNA structural parameters.

Main Methods:

  • Input of DNA sequences (A, C, G, T) for analysis.
  • Generation of nucleosome energy diagrams and coarse-grained chromatin representations.
  • Calculation and plotting of helical parameters (Tilt, Roll, Twist, Shift, Slide, Rise).
  • User selection of energy models, nucleosome structures, and placement methods.
  • Option to incorporate experimental nucleosome footprint data for array creation.

Main Results:

  • The default energy model shows a 0.7 correlation with experimental stability data.
  • Accurate prediction of six positioned nucleosomes in the mouse mammary tumor virus (MMTV) promoter.
  • Generation of nucleosome energy diagrams, chromatin models, and helical parameter plots.

Conclusions:

  • ICM Web is a valuable interactive tool for studying nucleosome stability and chromatin folding.
  • The server facilitates research on DNA sequences up to tens of kilobases.
  • No login is required, enhancing accessibility for researchers worldwide.