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\appendix
\section{References}
\raggedright

\begin{description}

\item [WHAT IF]

G.Vriend,
{\em WHAT IF: a molecular modelling and drug design program}
J. Mol. Graph. {\bf 8} 52--56 (1990).

\item [WHAT\_CHECK (verification routines from WHAT IF)]

R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
{\em Errors in protein structures}
Nature {\bf 381}, 272 (1996).
(see http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra information)

\item [Bond lengths and angles, protein residues]

R.Engh and R.Huber,
{\em Accurate bond and angle parameters for X-ray protein structure refinement}
Acta Crystallogr. {\bf A47}, 392--400 (1991).

\item [Bond lengths and angles, DNA/RNA]

G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Br\"unger and H.Berman,
{\em New parameters for the refinement of nucleic acid-containing structures}
Acta Crystallogr. {\bf D52}, 57--64 (1996).

\item [DSSP] 

W.Kabsch and C.Sander, 
{\em Dictionary of protein secondary structure: pattern
     recognition of hydrogen bond and geometrical features} 
Biopolymers {\bf 22}, 2577--2637 (1983).

\item [Hydrogen bond networks]

R.W.W.Hooft, C.Sander and G.Vriend,
{\em Positioning hydrogen atoms by optimizing hydrogen bond networks in
protein structures}
PROTEINS, {\bf 26}, 363--376 (1996).

\item [Matthews' Coefficient]

B.W.Matthews,
{\em Solvent Content of Protein Crystals}
J. Mol. Biol, {\bf 33}, 491--497 (1968).

\item [Protein side chain planarity]

R.W.W. Hooft, C. Sander and G. Vriend,
{\em Verification of protein structures: side-chain planarity}
J. Appl. Cryst, {\bf 29}, 714--716 (1996).

\item [Puckering parameters]

D.Cremer and J.A.Pople,
{\em A general definition of ring puckering coordinates}
J. Am. Chem. Soc. {\bf 97}, 1354--1358 (1975).

\item [Quality Control]

G.Vriend and C.Sander,
{\em Quality control of protein models: directional atomic 
     contact analysis}
J. Appl. Cryst. {\bf 26}, 47--60 (1993).

\item [Ramachandran plot]

G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan.
{\em Stereochemistry of Polypeptide Chain Conformations}
J. Mol. Biol. {\bf 7} 95--99 (1963).

\item [Symmetry Checks]

R.W.W.Hooft, C.Sander and G.Vriend,
{\em Reconstruction of symmetry related molecules from protein 
     data bank {(PDB)} files}
J. Appl. Cryst. {\bf 27}, 1006--1009 (1994).

\item [Ion Checks]

I.D.Brown and K.K.Wu,
{\em Empirical Parameters for Calculating Cation-Oxygen Bond Valences}
Acta Cryst. B {\bf 32}, 1957--1959 (1975).

M.Nayal and E.Di Cera,
{\em Valence Screening of Water in Protein Crystals Reveals Potential Na+ 
     Binding Sites}
J. Mol. Biol. {\bf 256} 228--234 (1996).

P.Mueller, S.Koepke and G.M.Sheldrick,
{\em Is the bond-valence method able to identify metal atoms in protein
     structures?}
Acta Cryst. D {\bf 59} 32--37 (2003).

\item [Checking checks]

K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al. 
{\em Who checks the checkers}
J. Mol. Biol. {\bf 276} 417--436 (1998).

\end{description}
\end{document}
