KOSMOS

Introduction

KOSMOS is the first web server to provide the structural biology community with both harmonic and anharmonic analyses of macromolecular structures including DNA, RNA, and Proteins. Online users can request thermal fluctuation study or transient pathway generation by simply submitting PDB ID or uploading personal data files through the query page. All the simulation outputs have been deposited into NMA and ENI database where most of data are disclosed to the public unless users request to limit accessibility to their data. Users can also enjoy versatility of KOSMOS through advanced query by utilizing several unique applications of elastic network models for their own purpose.

Harmonic - Normal Mode Analysis (NMA)

Normal mode analysis (NMA) is a useful tool to understand the harmonic behaviors (thermal fluctuations) of a macromolecule around its equilibrium. It is widely believed that a few lowest modes dominantly contribute to the global and collective motions of the system. We define the simplest Hookean potential energy and then solve the eigenproblem to determine the lowest modes. For large macromolecular structures having more than several thousand residues, the coarse-grained elastic network model has been explored to produce the lowest modes within reasonable time on a PC.

Anharmonic (Pathway Generation) - Elastic Network Interpolation (ENI)

Elastic Network Interpolation (ENI) is a useful tool to generate the anharmonic pathways for conformational transitions between two metastable conformations of the same macromolecule. In ENI, we do not interpolate Cartesian or internal coordinates, but rather the two sets of distances between spatially close representative atoms so that unrealistic conformations and steric clashes become less likely.

Getting Start!

Please be aware that NMA DB and ENI DB contain all simulation results of PDBs previously requested. KOSMOS user is strongly recommended to search PDB ID of interest from either NMA DB or ENI DB before requesting a simulation through QUERY. It will be very helpful for us to manage KOSMOS effectively and efficiently.

• QUERY: Input window for both NMA and ENI online simulations
• NMA DB: Normal Mode Analysis database including mode shape animation, downloadable eigenvalue and eigenvector dataset, linking matrix, two types of B-factor calculation, and residue fluctuation plot
• ENI DB: Elastic Network Interpolation database including conformational pathway animation, downloadable intermediate conformation data set, minimum distance plot (evidence of no steric clash) , and cost plot (semi evidence of energy barrier between two conformations)
• TUTORIAL: Brief description on various elastic network models, NMA, and ENI with downloadable example codes

Computational Bioengineering Lab. School of Mechanical Engineering & Department of Nano Science and Technology
Rm 22106. Sungkyunkwan Univ. 300. Chunchun-Dong. Jangan-Gu. 440-746. Korea,
E-mail : qktndn@skku.edu