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@ARTICLE{Giorgetti:201302,
      author       = {Giorgetti, Alejandro and Ruggerone, Paolo and Pantano,
                      Sergio and Carloni, Paolo},
      title        = {{A}dvanced {C}omputational {M}ethods in {M}olecular
                      {M}edicine},
      journal      = {Journal of biomedicine and biotechnology},
      volume       = {2012},
      issn         = {1110-7251},
      address      = {Cuyahoga Falls, Ohio},
      reportid     = {FZJ-2015-03607},
      pages        = {1 - 2},
      year         = {2012},
      abstract     = {The dauntingly complex functioning of human cells is often
                      the outcome of several molecular processes. Understanding
                      such processes is crucial for modern drug discovery,
                      defining interaction cascades, assessing the effects of
                      mutations changes in local concentrations of ligands, and so
                      forth. Computational methods, from systems biology to
                      bioinformatics and molecular simulation, allow to access
                      features difficult or impossible to be measured. Models (if
                      properly validated against experimental data) help
                      understand the intricate molecular mechanisms of life
                      processes. Bolstering the predictive power of these models
                      calls upon the computational biologist to improve algorithms
                      and methods. This issue reports on procedures and on
                      applications facing current challenges in computational
                      biology.Modern biological sciences are becoming more and
                      more multidisciplinary. At the same time, theoretical and
                      computational approaches gain in reliability and their field
                      of application widens. O. Fisette at al. discuss recent
                      advances in the areas of solution nuclear magnetic resonance
                      (NMR) spectroscopy and molecular dynamics (MD) simulations
                      that were made possible by the synergistic combination of
                      both methods.Interaction of proteins is of vital importance
                      for many cellular processes and when altered may cause
                      significant health problems, thus the availability of
                      reliable tools to predict and study the determinants of
                      protein-protein interactions is needed. In this regard, X.
                      -Y. Meng et al. present a newly adapted, computationally
                      efficient Brownian Dynamics- (BD-) based protein docking
                      method for predicting native protein complexes. The approach
                      includes global BD conformational sampling, compact complex
                      selection, and local energy minimization. A shell-based grid
                      force field represents the receptor protein and solvation
                      effects, partially considering protein flexibility.Hybrid
                      quantum mechanics/molecular mechanics (QM/MM) calculations
                      are routinely used to study quantum mechanical processes in
                      biological systems. J. Kang et al. present a review paper
                      describing an UNIX shell-based interface program connecting
                      two widely used QM and MM calculation engines, GAMESS and
                      AMBER. The tool was used to investigate a metalloenzyme,
                      azurin, and PU.1-DNA complex and mechanisms of hydrolysis
                      (editing reaction) in leucyl-tRNA synthetase complexed with
                      the mis-aminoacylated tRNALeu. The authors investigate the
                      influence of environmental effects on the electronic
                      structure.Electron transfer in proteins constitutes key
                      steps in several biological processes, ranging from
                      photosynthesis to aerobic respiration. T. Hayashi and A.
                      Stuchebrukhov investigate electron tunneling in
                      NADH : ubiquinone oxidoreductase (Complex I), a key
                      enzyme in cellular respiration as an entry point of the
                      electron transport chain of mitochondria and bacteria, by
                      evaluating the transition flux between donor and acceptor at
                      atomistic resolution. The study suggests that the diffusion
                      of internal water molecules dynamically controls tunneling
                      efficiency.},
      cin          = {GRS / IAS-5},
      ddc          = {610},
      cid          = {I:(DE-Juel1)GRS-20100316 / I:(DE-Juel1)IAS-5-20120330},
      pnm          = {899 - ohne Topic (POF2-899)},
      pid          = {G:(DE-HGF)POF2-899},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000304938400001},
      doi          = {10.1155/2012/709085},
      url          = {https://juser.fz-juelich.de/record/201302},
}