ArticleNucleic acids research2010
ICM Web: the interactive chromatin modeling web server.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 30 citations in OpenAlex.
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- Direct delivery of Cas9 or base editor protein and guide RNA complex enables genome editing in the retina.Molecular therapy. Nucleic acids · 2024Article
- The nucleosome reference frame and standard geometries for octasomes.Biophysical reviews · 2024Review
- Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?Biophysical reviews · 2021Review
- The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome.Nucleic acids research · 2021Article
- Genome Dashboards: Framework and Examples.Biophysical journal · 2020Article
- iNuc-ext-PseTNC: an efficient ensemble model for identification of nucleosome positioning by extending the concept of Chou's PseAAC to pseudo-tri-nucleotide composition.Molecular genetics and genomics : MGG · 2019Article
- Chromatin Higher-Order Folding: A Perspective with Linker DNA Angles.Biophysical journal · 2018Review
- Oligodeoxynucleotides Can Transiently Up- and Downregulate CHS Gene Expression in Flax by Changing DNA Methylation in a Sequence-Specific Manner.Frontiers in plant science · 2017Article
- Prediction of nucleosome positioning by the incorporation of frequencies and distributions of three different nucleotide segment lengths into a general pseudo k-tuple nucleotide composition.Bioinformatics (Oxford, England) · 2017Article
- Mechanisms underlying epigenetic and transcriptional heterogeneity in Chinese hamster ovary (CHO) cell lines.BMC biotechnology · 2016Article
- Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence.PloS one · 2015Article
- nuMap: a web platform for accurate prediction of nucleosome positioning.Genomics, proteomics & bioinformatics · 2014Article
- Structure-driven homology pairing of chromatin fibers: the role of electrostatics and protein-induced bridging.Journal of biological physics · 2013Article
- Dissecting epigenetic silencing complexity in the mouse lung cancer suppressor gene Cadm1.PloS one · 2012Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
The interactive chromatin modeling web server (ICM Web) is an interactive tool that allows users to rapidly assess nucleosome stability and fold sequences of DNA into putative chromatin templates. ICM Web takes a sequence composed of As, Cs, Gs, and Ts as input and generates (i) a nucleosome energy level diagram, (ii) coarse-grained representations of free DNA and chromatin and (iii) plots of the helical parameters (Tilt, Roll, Twist, Shift, Slide and Rise) as a function of position. The user can select from several different energy models, nucleosome structures and methods for placing nucleosomes in the energy landscape. Alternatively, if nucleosome footprints are known from experiment, ICM Web can use these positions to create a nucleosome array. The default energy model achieves a correlation coefficient of 0.7 with 100 experimentally determined values of stability and properly predicts the location of six positioned nucleosomes in the mouse mammary tumor virus (MMTV) promoter. ICM Web is suitable for interactively investigating nucleosome stability and chromatin folding for sequences up to tens of kilobases in length. No login is required to use ICM Web.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.