\begin{enumerate}

\item
{\v{S}}ali, A. and Blundell, T.~L.
 Definition of general topological equivalence in protein structures:
  A procedure involving comparison of properties and relationships through
  simulated annealing and dynamic programming.
 {\em J. Mol. Biol.}{ \bf 212}, 403--428 (1990).

\item
{\v{S}}ali, A., Overington, J.~P., Johnson, M.~S., and Blundell, T.~L.
 From comparisons of protein sequences and structures to protein
  modelling and design.
 {\em TIBS}{ \bf 15}, 235--240 (1990).

\item
Johnson, M.~S., {\v{S}}ali, A., and Blundell, T.~L.
 Phylogenetic relationships from three-dimensional protein structures.
 {\em Meth. Enzymol.}{ \bf 183}, 670--690 (1990).

\item
Johnson, M.~S., Overington, J.~P., and {\v{S}}ali, A.
 Knowledge-based protein modelling: Human plasma kallikrein and human
  neutrophil defensin.
 In {\em Current Research in Protein Chemistry: Techniques Structure
  and Function, }Villafranca, J.~J., editor,  567--574. Academic Press, Inc.,
  San Diego (1990).

\item
{\v{S}}ali, A.
 {\em Modelling three-dimensional structure of proteins from their
  sequence of amino acid residues}.
 PhD thesis, University of London, London,  (1991).

\item
{\v{S}}ali, A. and Blundell, T.~L.
 Comparative protein modelling by satisfaction of spatial restraints.
 {\em J. Mol. Biol.}{ \bf 234}, 779--815 (1993).

\item
{\v{S}}ali, A., Matsumoto, R., McNeil, H.~P., Karplus, M., and Stevens, R.~L.
 Three-dimensional models of four mouse mast cell chymases.
  {I}dentification of proteoglycan-binding regions and protease-specific
  antigenic epitopes.
 {\em J. Biol. Chem.}{ \bf 268}, 9023--9034 (1993).

\item
{\v{S}}ali, A. and Blundell, T.~L.
 Comparative protein modelling by satisfaction of spatial restraints.
 In {\em Protein Structure by Distance Analysis, }Bohr, H. and Brunak,
  S., editors,  64--86. IOS Press, Amsterdam (1994).

\item
{\v{S}}ali, A. and Overington, J.
 Derivation of rules for comparative protein modeling from a database
  of protein structure alignments.
 {\em Protein Sci.}{ \bf 3}, 1582--1596 (1994).

\item
{\v{S}}ali, A.
 {MODELER}: Implementing {3D} protein modeling.
 In {\em $mc^2$}, volume~2, ~5. Molecular Simulations Inc.,
  Burlington, MA (1995).

\item
Matsumoto, R., {\v{S}}ali, A., Ghildyal, N., Karplus, M., and Stevens, R.~L.
 Packaging of proteases and proteoglycans in the granules of mast
  cells and other hematopoietic cells. {A} cluster of histidines in mouse mast
  cell protease-7 regulates its binding to heparin serglycin proteoglycan.
 {\em J. Biol. Chem.}{ \bf 270}, 19524--19531 (1995).

\item
{\v{S}}ali, A.
 Protein modeling by satisfaction of spatial restraints.
 {\em Molecular Medicine Today}{ \bf 1}, 270--277 (1995).

\item
{\v{S}}ali, A., Potterton, L., Yuan, F., van Vlijmen, H., and Karplus, M.
 Evaluation of comparative protein structure modeling by {MODELLER}.
 {\em Proteins}{ \bf 23}, 318--326 (1995).

\item
{\v{S}}ali, A.
 Modelling mutations and homologous proteins.
 {\em Curr. Opin. Biotech.}{ \bf 6}, 437--451 (1995).

\item
Sheng, Y., {\v{S}}ali, A., Herzog, H., Lahnstein, J., and Krilis, S.
 Modelling, expression and site-directed mutagenesis of human
  $\beta_2$-glycoprotein {I}: {I}dentification of the major phospholipid
  binding site.
 {\em J. Immunol.}{ \bf 157}, 3744--3751 (1996).

\item
Ghildyal, N., Friend, D.~S., Stevens, R.~L., Austen, K.~F., Huang, C., Penrose,
  J., {\v{S}}ali, A., and Gurish, M.~F.
 Fate of two mast cell tryptases following passive systemic
  anaphylaxis of {BALB/c} and {V3} mastocytosis mice. {P}rolonged retention of
  exocytosed {mMCP-6} in connective tissues and rapid accumulation of
  enzymatically active {mMCP-7} in the blood chymases.
 {\em J. Exp. Med.}{ \bf 184}, 1061--1073 (1996).

\item
Xu, L.~Z., S{\'{a}}nchez, R., {\v{S}}ali, A., and Heintz, N.
 Ligand specificity of brain lipid binding protein.
 {\em J.Biol.Chem.}{ \bf 271}, 24711--24719 (1996).

\item
Wu, S., de~Lencastre, H., {\v{S}}ali, A., and Tomasz, A.
 A phosphoglucomutase-like gene essential for the optimal expression
  of methicillin resistance in {{\em Staphylococcus aureus}}: Molecular cloning
  and {DNA} sequencing.
 {\em Microbial Drug Resistance}{ \bf 2}, 277--286 (1996).

\item
Huang, C., Wong, G.~W., Ghildyal, N., Gurish, M.~F., {\v{S}}ali, A., Matsumoto,
  R., Qiu, W.-T., and Stevens, R.~L.
 The tryptase, mouse mast cell protease 7, exhibits anticoagulant
  activity {{\em in vivo}} and {{\em in vitro}} due to its ability to degrade
  fibrinogen in the presence of the diverse array of protease inhibitors in
  plasma.
 {\em J. Biol. Chem.}{ \bf 272}, 31885--31893 (1997).

\item
S{\'{a}}nchez, R. and {\v{S}}ali, A.
 Comparative protein modeling as an optimization problem.
 {\em Journal of Molecular Structure (Theochem)}{ \bf 398}, 489--496
  (1997).

\item
S{\'{a}}nchez, R. and {\v{S}}ali, A.
 Advances in comparative protein-structure modeling.
 {\em Curr. Opin. Struct. Biol.}{ \bf 7}, 206--214 (1997).

\item
Koulich, D., Orlova, M., Malhotra, A., {\v{S}}ali, A., Darst, S.~A., and
  Borukhov, S.
 Domain organization of {{\em {E}scherichia coli}} transcript cleavage
  factors {GreA} and {GreB}.
 {\em J. Biol. Chem.}{ \bf 272}, 7201--7210 (1997).

\item
Hunt, J.~E., Friend, D.~S., Gurish, M.~F., Feyfant, E., {\v{S}}ali, A., Huang,
  C., Ghildyal, N., Stechshulte, S., Austen, K.~F., and Stevens, R.~L.
 Mouse mast cell protease {(mMCP)} 9, a novel member of the chromosome
  14 family of serine proteases that is selectively expressed in uterine mast
  cells.
 {\em J. Biol. Chem.}{ \bf 46}, 29158--29166 (1997).

\item
S{\'{a}}nchez, R. and {\v{S}}ali, A.
 Evaluation of comparative protein structure modeling by {MODELLER-3}.
 {\em Proteins}{ \bf Suppl. 1}, 50--58 (1997).

\item
Guenther, B., Onrust, R., {\v{S}}ali, A., O'Donnell, M., and Kuriyan, J.
 Crystal structure of the {$\delta$'} subunit of the clamp-loader
  complex of {{\em E. coli}} {DNA} polymerase {III}.
 {\em Cell}{ \bf 91}, 335--345 (1997).

\item
S{\'{a}}nchez, R., Badretdinov, A.~Y., Feyfant, E., and {\v{S}}ali, A.
 Homology protein structure modeling.
 {\em Transactions Amer. Cryst. Assoc.}{ \bf 32}, 81--91 (1997).

\item
S{\'a}nchez, R. and {\v{S}}ali, A.
 Comparative protein structure modeling: Introduction and practical
  examples with {{\sc Modeller}}.
 In {\em Protein Structure Prediction: Methods and Protocols,
  }Webster, D.~M., editor,  97--129. Humana Press (2000).

\item
Huang, C., {\v{S}ali}, A., and Stevens, R.~L.
 Regulation and function of mast cell proteases in inflammation.
 {\em J. Clin. Immunol.}{ \bf 18}, 169--183 (1998).

\item
Kandiah, D.~A., {\v{S}ali}, A., Sheng, Y., Victoria, E.~J., Marquis, D.~M.,
  Coutts, S.~M., and Krilis, S.
 Current insights into the antiphospholipid syndrome: Clinical,
  immunological and molecular aspects.
 {\em Adv. Immunol.}{ \bf 70}, 507--563 (1998).

\item
Wolf, E., Vassilev, A., Makino, Y., {\v{S}}ali, A., Nakatani, Y., and Burley,
  S.~K.
 Crystal structure of a {GCN5}-related {N}-acetyltransferase: {{\em
  {S}erratia marcescens}} aminoglycoside 3-{N}-acetyltransferase.
 {\em Cell}{ \bf 94}, 51--61 (1998).

\item
S{\'a}nchez, R. and {\v{S}}ali, A.
 Large-scale protein structure modeling of the {{\em {S}accharomyces
  cerevisiae}} genome.
 {\em Proc. Natl. Acad. Sci. USA}{ \bf 95}, 13597--13602 (1998).

\item
{\v{S}}ali, A.
 100,000 protein structures for the biologist.
 {\em Nat. Struct. Biol.}{ \bf 5}, 1029--1032 (1998).

\item
S{\'{a}}nchez, R. and {\v{S}}ali, A.
 {{\sc ModBase}} : A database of comparative protein structure models.
 {\em Bioinformatics}{ \bf 15}, 1060--1061 (1999).

\item
Fiser, A., S{\'{a}}nchez, R., Melo, F., and {\v{S}}ali, A.
 Comparative protein structure modeling.
 In {\em Computational Biochemistry and Biophysics, in press,
  }Watanabe, M., Roux, B., MacKerell, A., and Becker, O., editors. Marcel
  Dekker (2000).

\item
S{\'a}nchez, R. and {\v{S}}ali, A.
 Comparative protein structure modeling in genomics.
 {\em J. Comp. Phys.}{ \bf 151}, 388--401 (1999).

\item
Wu, G., Fiser, A., ter Kuile, B., {\v{S}}ali, A., and M{\"{u}}ller, M.
 Convergent evolution of {{\em Trichomonas vaginalis}} lactate
  dehydrogenase from malate dehydrogenase.
 {\em Proc. Natl. Acad. Sci. USA}{ \bf 96}, 6285--6290 (1999).

\item
Nagata, T., Gupta, V., Kim, W.-Y., {\v{S}}ali, A., Chait, B.~T., Shigesada, K.,
  Ito, Y., and Werner, M.~H.
 Immunoglobulin motif {DNA} recognition and heterodimerization for the
  {PEBP2/CBF} {Runt}--domain.
 {\em Nat. Str. Biol.}{ \bf 6}, 615--619 (1999).

\item
Miwa, J.~M., {Ibanez-Tallon}, I., Crabtree, G.~W., S\'{a}nchez, R., {\v{S}}ali,
  A., Role, L.~W., and Heintz, N.
 lynx1, an endogenous toxin-like modulator of nicotinic acetylcholine
  receptors in the mammalian {CNS}.
 {\em Neuron}{ \bf 23}, 105--114 (1999).

\item
Huang, C., Morales, G., Vagi, A., Chanasyk, K., Ferrazzi, M., Burklow, C., Qiu,
  W.~T., Feyfant, E., {\v{S}}ali, A., and Stevens, R.~L.
 Formation of enzymatically active, homotypic and heterotypic
  tetramers of mouse mast cell tryptases.
 {\em J. Biol. Chem.}{ \bf 275}, 351--358 (2000).

\item
Wong, G.~W., Tang, Y., Feyfant, E., {\v{S}}ali, A., Huang, C., and Stevens,
  R.~L.
 Identification of a new tryptase in mice and humans which possesses a
  novel {C}-terminal, membrane spanning segment.
 {\em J. Biol. Chem.}{ \bf 274}, 30784--30793 (1999).

\item
Wu, G., Morrison, H.~G., Fiser, A., McArthur, A.~G., {\v{S}}ali, A., Sogin,
  M.~L., and M{\"{u}}ller, M.
 Core histones of the amitochondriate protist, {{\em Giardia
  lamblia}}.
 {\em Mol. Biol. Evol.}{ \bf 17}, 1156--1163 (2000).

\item
Burley, S.~K., Almo, S.~C., Bonanno, J.~B., , Capel, M., Chance, M.~R.,
  Gaasterland, T., Lin, D., {\v{S}}ali, A., Studier, F.~W., and Swaminathan, S.
 Structural genomics: beyond the {H}uman {G}enome {P}roject.
 {\em Nat. Genet.}{ \bf 23}, 151--157 (1999).

\item
Mart\'{\i}-Renom, M.~A., Stuart, A., Fiser, A., S{\'{a}}nchez, R., Melo, F.,
  and {\v{S}}ali, A.
 Comparative protein structure modeling of genes and genomes.
 {\em Ann. Rev. Biophys. Biomolec. Struct.}{ \bf 29}, 291--325 (2000).

\item
S{\'{a}}nchez, R., Pieper, U., Mirkovi\'{c}, N., de~Bakker, P. I.~W.,
  Wittenstein, E., and {\v{S}}ali, A.
 {{\sc ModBase}}, a database of annotated comparative protein
  structure models.
 {\em Nucl. Acids Res.}{ \bf 28}, 250--253 (2000).

\item
{\v{S}}ali, A. and Kuriyan, J.
 Challenges at the frontiers of structural biology.
 {\em Trends Biochem. Sci.}{ \bf 22}, M20--M24 (1999).

\item
Pieper, U., Eswar, N., S{\'{a}}nchez, R., Mirkovi{\'{c}}, N., Lane, W., Sammut,
  M., John, B., and {\v{S}}ali, A.
 {{\sc ModBase}}, a database of annotated comparative protein
  structure models.
 {\em Nucl. Acids Res.}{ \bf }, in press (2001).

\item
Groft, C.~M., Beckmann, R., {\v{S}}ali, A., and Burley, S.~K.
 Crystal structures of ribosome anti-association factor {IF6}.
 {\em Nat. Struct. Biol.}{ \bf 7}, 1156--1164 (2000).

\item
S\'{a}nchez, R., Pieper, U., Melo, F., Eswar, N., Mart\'{\i}-Renom, M.,
  Madhusudhan, M., Mirkovi{\'{c}}, N., and {\v{S}}ali, A.
 Protein structure modeling for structural genomics.
 {\em Nat. Struct. Biol.}{ \bf 7}, 986--990 (2000).

\item
Fiser, A., Do, R. K.~G., and {\v{S}}ali, A.
 Modeling of loops in protein structures.
 {\em Protein Science}{ \bf 9}, 1753--1773 (2000).

\end{enumerate}
