ArticleNucleic acids research2012
KOSMOS: a universal morph server for nucleic acids, proteins and their complexes.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 32 citations in OpenAlex.
- Tackling Hysteresis in Conformational Sampling: How to Be Forgetful with MEMENTO.Journal of chemical theory and computation · 2023Article
- Disorder-Order Transitions in Conformational Selection of a Peptide by Ebola Virus Nucleoprotein.ACS omega · 2020Article
- Large-Scale Conformational Changes and Protein Function: Breaking theFrontiers in molecular biosciences · 2019Review
- DynOmics: dynamics of structural proteome and beyond.Nucleic acids research · 2017Article
- Article
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- MMB-GUI: a fast morphing method demonstrates a possible ribosomal tRNA translocation trajectory.Nucleic acids research · 2016Article
- iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics.Nucleic acids research · 2016Article
- Computational Simulation of the Activation Cycle of Gα Subunit in the G Protein Cycle Using an Elastic Network Model.PloS one · 2016Article
- WEBnm@ v2.0: Web server and services for comparing protein flexibility.BMC bioinformatics · 2014Article
- iMODS: internal coordinates normal mode analysis server.Nucleic acids research · 2014Article
- Elastic network models capture the motions apparent within ensembles of RNA structures.RNA (New York, N.Y.) · 2014Article
- A mass weighted chemical elastic network model elucidates closed form domain motions in proteins.Protein science : a publication of the Protein Society · 2013Article
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2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
KOSMOS is the first online morph server to be able to address the structural dynamics of DNA/RNA, proteins and even their complexes, such as ribosomes. The key functions of KOSMOS are the harmonic and anharmonic analyses of macromolecules. In the harmonic analysis, normal mode analysis (NMA) based on an elastic network model (ENM) is performed, yielding vibrational modes and B-factor calculations, which provide insight into the potential biological functions of macromolecules based on their structural features. Anharmonic analysis involving elastic network interpolation (ENI) is used to generate plausible transition pathways between two given conformations by optimizing a topology-oriented cost function that guarantees a smooth transition without steric clashes. The quality of the computed pathways is evaluated based on their various facets, including topology, energy cost and compatibility with the NMA results. There are also two unique features of KOSMOS that distinguish it from other morph servers: (i) the versatility in the coarse-graining methods and (ii) the various connection rules in the ENM. The models enable us to analyze macromolecular dynamics with the maximum degrees of freedom by combining a variety of ENMs from full-atom to coarse-grained, backbone and hybrid models with one connection rule, such as distance-cutoff, number-cutoff or chemical-cutoff. KOSMOS is available at http://bioengineering.skku.ac.kr/kosmos.
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