Molecular docking using shape descriptors, J, vol.611 ,
, Comput Chem, vol.13, pp.380-397, 1992.
Automated docking with grid-based energy eval-613 uation, J Comput Chem, vol.13, pp.505-524, 1992. ,
, , p.615
DOCK 6: Combining techniques to model RNA-small 616 molecule complexes, RNA, vol.15, pp.1219-1230, 2009. ,
Areas, volumes, packing and protein structure, Annu Rev Biophys, vol.618, pp.151-176, 1977. ,
Solvent-accessible surfaces of proteins and nucleic acids, Science, vol.620, pp.709-713, 1983. ,
A geometric approach to 622 macromolecule-ligand interactions, J Mol Biol, vol.161, pp.269-88, 1982. ,
Continuum 624 solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices, J 625 Am Chem Soc, vol.120, pp.9401-9409, 1998. ,
, , vol.627
,
, Calculating structures and free energies of complex molecules: combining molecular 629 mechanics and continuum models, Acc Chem Res, vol.33, pp.889-897, 2000.
Pairwise solute descreening of solute charges 631 from a dielectric medium, Chem Phys Lett, vol.246, pp.122-129, 1995. ,
Parametrized models of aqueous free energies 633 of solvation based on pairwise descreening of solute atomic charges from a dielectric 634 medium, J Phys Chem, vol.100, 1996. ,
Estimation of absolute free energies 636 of hydration using continuum methods: accuracy of partial charge models and opti-637 mization of nonpolar contributions, J Chem Theo Comput, vol.2, pp.128-139, 2006. ,
Maps for the visualization of high-dimensional data spaces, Proc. 639 Workshop on Self organizing Maps, pp.225-230 ,
U*-matrix: a tool to visualize clusters in high dimensional data, Fach-641 bereich Mathematik und Informatik, 2003. ,
Conformational and functional 643 analysis of molecular dynamics trajectories by Self-Organising Maps. BMC bioin-644 formatics, vol.12, p.158, 2011. ,
Direct molecular 646 dynamics observation of protein folding transition state ensemble, Biophys J, vol.647, pp.3525-3532, 2002. ,
VMD -Visual Molecular Dynamics, J Mol, vol.649, pp.33-38, 1996. ,
A convective replica-exchange method for sampling 651 new energy basins, J Comput Chem, vol.34, pp.132-140, 2013. ,
Transition path sampling: Throw-653 ing ropes over rough mountain passes, in the dark, Ann Rev Phys Chem, vol.53, pp.291-318, 2002. ,
Improved sampling methods for molecular simulation, Curr Opin, vol.656 ,
, Struct Biol, vol.17, pp.187-191, 2007.
Enhanced sampling algorithms, Methods Mol 658 Biol, vol.924, pp.153-195, 2013. ,
Vanden-Eijnden, E. Transition pathways in complex 660 systems: Reaction coordinates, isocommittor surfaces, and transition tubes, p.661 ,
, Phys Lett, vol.413, pp.242-247, 2005.
Function of the D 663 alanine: D-alanine ligase lid loop: a Molecular Modeling and Bioactivity Study, J, vol.664 ,
, Med Chem, vol.55, pp.6849-6856, 2012.
, Systems used for MD simulations
, X-ray structures used in MD simulations