A theoretical study of protein docking to self-assembled monolayers using a new approach is presented. Docking experiments based on space complementarity implemented in FTDock software were performed for three different proteins: tubulin dimer, cytochrome c, and lysozyme. The proteins were adsorbed on alkanethiol surfaces with different terminating groups and 50 000 best orientations of each protein were analyzed. For all systems three filters based on different chemical and biological approaches were applied. Correctly docked proteins for the cytochrome c and lysozyme systems were found in a list of the first 12 results after applying the geometrical and grouping filter and in a list of the first 3 results after applying the biological filter. We have found that alkanethiol monolayers with odd and even numbers of -CH2- groups have similar properties in terms of interactions with the two proteins. Docking of the tubulin dimer revealed that the orientation favored from the applicational point of view can be found in a list of the first 14 results for monolayers with different terminating groups and that there may be a noticeable difference in tubulin dimer interactions with alkanethiol chains of various length. The results for tubulin dimer docking combined with microtubules ability of reversible assembly suggest that these biological structures may become good candidates to serve as templates for fabrication of nanowires and other nanoscale electronic devices. The new method of theoretical docking presented may be used as a fast and reliable tool complementing other theoretical and experimental techniques of exploring other protein-surface interfaces.