TY - JOUR AU - Chavent, M. AU - Duncan, A. L. AU - Sansom, M. S. PY - 2016 DA - 2016// TI - Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale JO - Curr Opin Struct Biol VL - 40 UR - https://doi.org/10.1016/j.sbi.2016.06.007 DO - 10.1016/j.sbi.2016.06.007 ID - Chavent2016 ER - TY - JOUR AU - Hinsen, K. PY - 2000 DA - 2000// TI - The molecular modeling toolkit: a new approach to molecular simulations JO - J Comput Chem VL - 21 UR - https://doi.org/3.0.co;2-b DO - 3.0.co;2-b ID - Hinsen2000 ER - TY - JOUR AU - Roe, D. R. AU - Cheatham, T. E. PY - 2013 DA - 2013// TI - Ptraj and cpptraj: software for processing and analysis of molecular dynamics trajectory data JO - J Chem Theory Comput VL - 9 UR - https://doi.org/10.1021/ct400341p DO - 10.1021/ct400341p ID - Roe2013 ER - TY - JOUR AU - Doerr, S. AU - Harvey, M. J. AU - Noé, F. AU - Fabritiis, G. PY - 2016 DA - 2016// TI - Htmd: high-throughput molecular dynamics for molecular discovery JO - J Chem Theory Comput VL - 12 UR - https://doi.org/10.1021/acs.jctc.6b00049 DO - 10.1021/acs.jctc.6b00049 ID - Doerr2016 ER - TY - STD TI - Romo TD, Grossfield A. Loos: an extensible platform for the structural analysis of simulations. In: Engineering in medicine and biology society. 2009. pp. 2332–5. https://doi.org/10.1109/iembs.2009.5335065 ID - ref5 ER - TY - JOUR AU - Michaud-Agrawal, N. AU - Denning, E. J. AU - Woolf, T. B. AU - Beckstein, O. PY - 2011 DA - 2011// TI - Mdanalysis: a toolkit for the analysis of molecular dynamics simulations JO - J Comput Chem VL - 32 UR - https://doi.org/10.1002/jcc.21787 DO - 10.1002/jcc.21787 ID - Michaud-Agrawal2011 ER - TY - JOUR AU - McGibbon, R. T. AU - Beauchamp, K. A. AU - Harrigan, M. P. AU - Klein, C. AU - Swails, J. M. AU - Hernandez, C. X. AU - Schwantes, C. R. AU - Wang, L. -. P. AU - Lane, T. J. AU - Pande, V. S. PY - 2015 DA - 2015// TI - Mdtraj: a modern open library for the analysis of molecular dynamics trajectories JO - Biophys J VL - 109 UR - https://doi.org/10.1016/j.bpj.2015.08.015 DO - 10.1016/j.bpj.2015.08.015 ID - McGibbon2015 ER - TY - JOUR AU - Yesylevskyy, S. O. PY - 2012 DA - 2012// TI - Pteros: fast and easy to use open-source c++ library for molecular analysis JO - J Comput Chem VL - 33 UR - https://doi.org/10.1002/jcc.22989 DO - 10.1002/jcc.22989 ID - Yesylevskyy2012 ER - TY - JOUR AU - Yesylevskyy, S. O. PY - 2015 DA - 2015// TI - Pteros 2.0: evolution of the fast parallel molecular analysis library for c++ and python JO - J Comput Chem VL - 36 UR - https://doi.org/10.1002/jcc.23943 DO - 10.1002/jcc.23943 ID - Yesylevskyy2015 ER - TY - JOUR AU - Humphrey, W. AU - Dalke, A. AU - Schulten, K. PY - 1996 DA - 1996// TI - Vmd: visual molecular dynamics JO - J Mol Graph VL - 14 UR - https://doi.org/10.1016/0263-7855(96)00018-5 DO - 10.1016/0263-7855(96)00018-5 ID - Humphrey1996 ER - TY - JOUR AU - Jeong, J. C. AU - Jo, S. AU - Wu, E. L. AU - Qi, Y. AU - Monje-Galvan, V. AU - Yeom, M. S. AU - Gorenstein, L. AU - Chen, F. AU - Klauda, J. B. AU - Im, W. PY - 2014 DA - 2014// TI - St-analyzer: a web-based user interface for simulation trajectory analysis JO - J Comput Chem VL - 35 UR - https://doi.org/10.1002/jcc.23584 DO - 10.1002/jcc.23584 ID - Jeong2014 ER - TY - JOUR AU - Hess, B. AU - Kutzner, C. AU - Spoel, D. AU - Lindahl, E. PY - 2008 DA - 2008// TI - Gromacs 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation JO - J Chem Theory Comput VL - 4 UR - https://doi.org/10.1021/ct700301q DO - 10.1021/ct700301q ID - Hess2008 ER - TY - JOUR AU - Efremov, R. G. AU - Chugunov, A. O. AU - Pyrkov, T. V. AU - Priestle, J. P. AU - Arseniev, A. S. AU - Jacoby, E. PY - 2007 DA - 2007// TI - Molecular lipophilicity in protein modeling and drug design JO - Curr Med Chem VL - 14 UR - https://doi.org/10.2174/092986707779941050 DO - 10.2174/092986707779941050 ID - Efremov2007 ER - TY - CHAP AU - Polyansky, A. A. AU - Volynsky, P. E. AU - Efremov, R. G. ED - Donev, R. PY - 2011 DA - 2011// TI - Structural, dynamic, and functional aspects of helix association in membranes: a computational view BT - Advances in protein chemistry and structural biology PB - Elsevier CY - Cambridge UR - https://doi.org/10.1016/b978-0-12-381262-9.00004-5 DO - 10.1016/b978-0-12-381262-9.00004-5 ID - Polyansky2011 ER - TY - JOUR AU - Bocharov, E. V. AU - Mineev, K. S. AU - Pavlov, K. V. AU - Akimov, S. A. AU - Kuznetsov, A. S. AU - Efremov, R. G. AU - Arseniev, A. S. PY - 2017 DA - 2017// TI - Helix-helix interactions in membrane domains of bitopic proteins: specificity and role of lipid environment JO - Biochim Biophys Acta Biomembr VL - 1859 UR - https://doi.org/10.1016/j.bbamem.2016.10.024 DO - 10.1016/j.bbamem.2016.10.024 ID - Bocharov2017 ER - TY - JOUR AU - Lundborg, M. AU - Apostolov, R. AU - Spangberg, D. AU - Gardenas, A. AU - Spoel, D. AU - Lindahl, E. PY - 2014 DA - 2014// TI - An efficient and extensible format, library, and api for binary trajectory data from molecular simulations JO - J Comput Chem VL - 35 UR - https://doi.org/10.1002/jcc.23495 DO - 10.1002/jcc.23495 ID - Lundborg2014 ER - TY - JOUR AU - Spangberg, D. AU - Larsson, D. S. AU - Spoel, D. PY - 2011 DA - 2011// TI - Trajectory ng: portable, compressed, general molecular dynamics trajectories JO - J Mol Model VL - 17 UR - https://doi.org/10.1007/s00894-010-0948-5 DO - 10.1007/s00894-010-0948-5 ID - Spangberg2011 ER -