Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions

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Team Project

Project title: "Development and integration of new multiscale modeling tools for molecular biology: structure, dynamics and thermodynamics"

Project period: Jul 2011 - June 2015

Research partners:

  • Institute of Crystallography of CNR (Consiglio Nazionale delle Ricerche) in Bari, Italy
  • International School for Advanced Studies (SISSA) in Trieste, Italy
  • The Research Institute at Nationwide Childrens Hospital, Columbus, USA


The main goal of the project: is to develop a new suite of bioinformatics molecular modeling tools for structure prediction and study of dynamics and thermodynamics of proteins, nucleic acids (and other biomolecules) and their assemblies. These tools will be integrated with the existing state-of-the-art computational tools of molecular biology and made available to the scientific community via a multifunctional web server.

In the last ten years or so automated web servers of various functionalities, aimed at solving typical problems of bioinformatics and computational structural biology, became increasingly popular. Such servers are very useful in the popularization of new computational methods and, what seems to be extremely important, made these advanced methods easily available to experimental biologists, pharmacologists, biotechnologists and other life science experts.

 

The "Development and integration of new multiscale modeling tools for molecular biology: structure, dynamics and thermodynamics" project is realized within the TEAM programme of Foundation for Polish Science, cofinanced from European Union, Regional Development Fund.

 

 

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Publications:

[15]
Author(s): S. Kmiecik; J. Wabik; M. Kolinski; M. Kouza; A. Koliński
Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, Springer Series in Bio-/Neuroinformatics, Adam Liwo, Ed., 1:55-79, 2014
[14]
Author(s): M. Blaszczyk; D. Gront; S. Kmiecik; K. Ziolkowska; M. Panek; A. Koliński
Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes, Springer Series in Bio-/Neuroinformatics, Adam Liwo, Ed., 1:25-53, 2014
[13]
Author(s): J.K. Noel; J.N. Onuchic; J.I. Sulkowska
The Journal of Physical Chemistry Letters, 4:3570-3573, 2013
[12]
Author(s): M. Kouza; C.K. Hu; M.Suan Li; A. Koliński
The Journal of Chemical Physics, 139:065103, 2013
[11]
Author(s): M. Blaszczyk; M. Jamroz; S. Kmiecik; A. Koliński
Nucleic Acids Research, 41:W406-W411, 2013
[10]
Author(s): J. Wabik; S. Kmiecik; D. Gront; M. Kouza; A. Koliński
International Journal of Molecular Sciences, 14:9893–9905, 2013
[9]
Author(s): M. Jamroz; M. Orozco; A. Koliński; S. Kmiecik
Journal of Chemical Theory and Computation, 9:119 - 125, 2013
[8]
Author(s): M. Jamroz; A. Koliński; S. Kmiecik
Nucleic Acids Research, 41:W427-W431, 2013
[7]
Author(s): M. Jamroz; A. Koliński
BMC Bioinformatics, 14:62, 2013
[6]
Author(s): P. Gniewek; A. Koliński; R.L. Jernigan; A. Kloczkowski
The Journal of Chemical Physics, 136:195101, 2012

Pages