... all

http://www2.ebi.ac.uk/pdb/

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... resource

http://scop.mrc-lmb.cam.ac.uk/scop/

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... CATH

http://www.biochem.ucl.ac.uk/bsm/cath/

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... site

http://www.biochem.ucl.ac.uk/bsm/cath/lex/cathinfo.html

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... correct?

Although, interestingly, 75% is actually three-quarters of the way between the random alignment $Q_3$ of 35% and 88%

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... Martin

http://www.biochem.ucl.ac.uk/~martin/PROGRAMS.TXT

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...ProFit

http://www.biochem.ucl.ac.uk/~martin/#programs

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...)

this is the solvent accessible contact surface area buried on complexing with antigen

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... class

based on a simple clustering of interface area

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... topography

combining site topography classification

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... TSA

transition state analogue

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... topography

combining site topography classification

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... internet

http://www.biochem.ucl.ac.uk/~martin/abs/GeneralInfo.html#contactdata

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... GRASP

GRASP macros are available from http://www.biochem.ucl.ac.uk/~bob/Ab/graspMacro.txt

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... alignments

often generated automatically using substitution matrices

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... series

http://www.mbi.ucla.edu/people/fischer/BENCH/benchmark1.html

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...)

This manipulation of the results is not completely valid. Ideally, the whole experiment should be repeated without any highly similar pairs, rather than just discarding their results as we have done here.

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... SOM\_PAK

source code available from http://nucleus.hut.fi/nnrc/nnrc-programs.html

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... trend

We need to verify that this is not an effect of sequence order, by mapping reversed or shuffled sequences. The order of training vector presentation should not affect the mapping.

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... internet

http://www.biochem.ucl.ac.uk/~bob/thesis/1sxaA0_anim.html

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... Web

http://www.biochem.ucl.ac.uk/bsm/cath/

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