Molecular modelling and simulations in cancer research |
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| Authors: | Ran Friedman Kjetil Boye Kjersti Flatmark |
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| Affiliation: | 1. Computational Chemistry and Biochemistry Group, School of Natural Sciences, Linnæus University, 391 82 Kalmar, Sweden;2. Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;3. Department of Oncology, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;4. Department of Gastroenterological Surgery, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway;5. Linnæus University, Biomaterials Chemistry Centre of Excellence, 391 82 Kalmar, Sweden |
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| Abstract: | The complexity of cancer and the vast amount of experimental data available have made computer-aided approaches necessary. Biomolecular modelling techniques are becoming increasingly easier to use, whereas hardware and software are becoming better and cheaper. Cross-talk between theoretical and experimental scientists dealing with cancer-research from a molecular approach, however, is still uncommon. This is in contrast to other fields, such as amyloid-related diseases, where molecular modelling studies are widely acknowledged. The aim of this review paper is therefore to expose some of the more common approaches in molecular modelling to cancer scientists in simple terms, illustrating success stories while also revealing the limitations of computational studies at the molecular level. |
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| Keywords: | AIMD, ab initio molecular dynamics AEP, asparagine endopeptidase ALK, anaplastic lymphoma kinase BD, Brownian dynamics CPMD, Car&ndash Parrinello molecular dynamics DFT, density functional theory DPD, dissipative particle dynamics ENM, elastic network model ERK2, extracellular signal-regulated kinase 2 EXAFS, extended X-ray absorption fine structure FRET, Fö rster resonance energy transfer L-ASN, l-asparaginase MD, molecular dynamics NMA, normal mode analysis QM, quantum mechanics QM/MM, quantum mechanics/molecular mechanics SAXS, small angle X-ray scattering YAS, yttrium-alumino-silicate |
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