10.1 Potential Developments

The matter as to what improvements are to be made to HOLE is up to the users. You are welcome to make improvements subject to the conditions set out in section 1.0. Please also try to remain within the programming philosophy of the rest of the program. In particular comments are very important to the usability of a piece of code and if a program hits an error it should produce a sensible error message and "die" elegantly not cause the operating system to produce an unintelligible message and useless "core" file. Please send me details of any changes made by email.

Please send me a copy of any publication using HOLE so that it can be added to this list.

Gramicidin A

Smart, O.S., Goodfellow, J.M., Wallace, B.A. (1993) The pore dimensions of gramicidin A, Biophys. J., 65:2455-2460.
Paper gives a description of the method. Application is made to the four experimentally determined structures of gramicidin A. These are the NMR structure for the channel form (determined by Arseniev A.S. et al. (1985) FEBS Lett. 186:168-174) and X-ray crystal structures for two different antiparallel double-helical pores (due to Langs, D.A. (1988) Science 241:188-191 and Wallace, B.A. & K. Ravikumar. (1988) Science 241:182-187).

Annexin V

Smart, O.S., Wallace, B.A., Goodfellow, J.M. (1994). Preliminary analysis of the pore dimensions of human annexin V. Biochem. Soc. Trans., 649:146s.
Preliminary application of HOLE to human annexin V crystal structure due to Huber et al. (1992) J. Mol. Biol. 223:683-704. Reveals the complicated topology of the pore through this interesting molecule.

Alamethicin

Breed, J., Sansom, M.S.P. (1994). Alamethicin channels modelled by simulated annealing and molecular dynamics. Biochem. Soc. Trans. 649:157s.

Bacteriorhodopsin

to be included in new paper

Porin

to be included in new paper

Must be updated!%%%