In Press

• D.A. Belinskaya1, A.H. Juffer, N.N. Shestakova, The role of electrostatic interactions in the process of ligand sorption into ChE active sites based on molecular modelling studies. Russian Journal of Bioorganic Chemistry.

2009

• S. Sharma and A.H. Juffer, Hydrolysis of Phosphohistidine Intermediate of Prostatic Acid Phosphatase. Chem. Commun. 6385-6387, 2009.
• T. Fukamizo, R. Miyake, A. Tamura, T. Ohnuma, K. Skriver, Niko V. Pursiainen, A.H. Juffer, A flexible loop controlling the enzymatic activity and specificity in a glycerol hydrolase family 19 endochitinase from barley seeds (Hordeum vulgare L.), Biochem. Biophys. Acta Proteins and Proteomics, 1794, 1159-1167, 2009
• S. Donnini, A. Villa, G. Groenhof, A. E. Mark, R.W. Wierenga, A.H. Juffer, Inclusion of ionization states of ligand in affinity calculations. Proteins 76, 138 - 150, 2009.

2008

• A.H. Juffer, U. Marina, O. Niemitalo, J. Koivukangas, Computer modeling of brain tumor growth (review). Mini Rev. Med. Chem. 8, 1494-506, 2008.
• S. Sharma, A. Rauk, A.H. Juffer, A DFT Study of Phosphohistidine Enzyme Intermediateon in Prostatic Acid Phosphatase. J. Am. Chem. Soc, 130, 9708 - 9716, 2008.
• Z.-J. Chen, R. Pudas, S. Sharma, O.S. Smart, A.H. Juffer, J.K. Hiltunen, R.K. Wierenga, A.M. Haapalainen, Structural Enzymological Studies of 2-Enoyl Thioester Reductase of the Human Mitochondrial FAS II Pathway: New Insights into Its Substrate Recognition Properties. J. Mol. Biol. 379, 830 - 844, 2008.

2007

• W Xin and A.H.Juffer, A boundary element formulation of protein electrostatics with explicit ions. J Comput Phys, 223, 416 - 435, 2007
• L. Settimo, S. Donnini, A.H. Juffer, R. Woody, O. Marin, A "mini-calmodulin" peptide as a protein model to study the conformational changes upon calcium binding and phosphorylation in the full-lenght calmodulin. Biopolymers, 88, 373-385, 2007.
• W.A Stanley, N.V. Pursiainen, E.F. Garman, A.H. Juffer, M. Wilmanns, P. Kursula, A previously unobserved conformation for the human Pex5p receptor suggests roles for intrinsic flexibility and rigid domain motions in ligand binding , BMC Structural Biology, 7, 24 - 35, 2007.
• R. Myllylä, C. Wang, J. Heikkinen, A.H. Juffer, O. Lampela, M. Risteli, H. Ruotsalainen, A. Salo, L. Sipilä, Expanding the Lysyl Hydroxylase Toolbox: New Insights into the localization and activities of Lysyl Hydroxylase 3 (LH3)., 212, 323 - 329, 2007.

2006

• S. Donnini, G Groenhof, R.K. Wierenga, A.H. Juffer, The planar conformation of a strained proline ring: a QM/MM study, Proteins, 64, 700-710, 2006
• M. S. Ylianttila, N.V. Pursiainen, A.H. Juffer, Y. Poirier, J.K. Hiltunen and T. Glumoff, Crystal structure of yeast peroxisomal multifunctional enzyme: Structural basis for substrate specificity of (3R)-hydroxyacyl-CoA dehydrogenase units. J Mol Biol, 358, 1286-1295, 2006

2005

• T. Ohnishi, A.H. Juffer, M. Tamoi, K. Skriver, T. Fukamizo, 26 kDa endochitinase from barley seeds: an interaction of the ionizable side chains essential for catalysis, J. Biochem. 138, 553-62, 2005
• O. Niemitalo, A. Neubauer, U. Liebal, J. Myllyharju, A.H. Juffer and P Neubauer, Modelling of translation of human protein disulfide isomerase in Escherichia coli. A case study of gene optimisation, J. Biotechnology, 120, 11-24, 2005.
• S. Sharma, P. Pirila, H. Kaija, P. Vihko and A.H. Juffer, Theoretical investigations of prostatic acid phosphatase, Proteins, 58, 295 - 308, 2005.
• S. Donnini, A. Mark, A.H. Juffer, and A. Villa, Incorporating the effect of ionic strength in free energy calculations using explicit ions, J. Comput. Chem., 26, 115 - 122, 2005.

2004

• M. Risteli, O. Niemitalo, H. Lankinen, A.H. Juffer, R. Myllylä, Characterization of collagenous peptides bound to lysyl hydroxylase isoforms., J. Biol. Chem., 279, 37535 - 37543, 2004
• A. M. Remes, S. Filppula, H. Rantala, J. Leisti, A. Ruokonen, S. Sharma, A.H. Juffer, and J. K. Hiltunen, A novel mutation of the fumarase gene in a family with autosomal recessive fumarase deficiency J. Mol. Medicine, 82, 550 - 554, 2004
• S. Donnini and A.H. Juffer, Calculation of affinities of peptides for proteins, J. Comput. Chem. 25, 393-411, 2004
• A.K. Lappi, M.F. Lensink, H.I. Alanen, K.E.H. Salo, M. Lobell, A.H. Juffer and L.W. Ruddock, A conserved arginine plays a role in the catalytic cycle of the protein disulphide isomerase, J. Mol. Biol. 335, 283-295, 2004.

2003

• O. Lampela, A.H. Juffer and A. Rauk, Conformational analysis of glutathione in aqueous solution with molecular dynamics. J. Phys. Chem. A., 107, 9208-9220, 2003.
• M. Suokas, O. Lampela, A.H. Juffer, R. Myllylä and S. Kellokumpu, Retrieval-independent localization of Lysyl Hydroxylase in the endoplasmic reticulum via a peptide fold in its iron binding domain. Biochem. J., 370, 913-920, 2003

2002

• M.F. Lensink, A.M. Haapalainen, J.K. Hiltunen, T. Glumoff and A.H. Juffer, Response of SCP-2L domain of human MFE-2 to ligand removal: Binding site closure and burial of peroxisomal targeting signal, J. Mol. Biol., 323, 99-113, 2002
• C.M. Shepherd, H.J. Vogel and A.H. Juffer, Monte Carlo and molecular dynamics studies of peptide-bilayer binding, in: High Performance Computing Systems and Applications 2000 (Nikitas J. Dimpoulos and Kin F. Li, Eds.), Kluwer Academic Publishers (Dordrechts, The Netherlands), Chapter 29, 447-464, 2002.

2001

• T. Fukamizo, A.H. Juffer and R. Brezinski, A local structure assisting the enzyme catalysis from behind the catalytic center. (In Japanese), Protein, Nulceic Acid, and Enzyme, 46, 1261-1267, 2001.
• C.M. Shepherd, K.A. Schaus, H.J. Vogel and A.H. Juffer, A Molecular Dynamics Study of Peptide-Bilayer Adsorption. Biophys. J. 80, 579-596 (2001)
• A.H. Juffer, C.M. Shepherd and H.J. Vogel, Protein-membrane electrostatic interactions: Application of the Lekner summation technique. J. Chem. Phys. 114, 1892-1905 (2001)

2000

• A.H. Juffer and H.J. Vogel, pK_a Calculations of Calbindin D_9k: Effects of Ca²⁺ Binding, Protein Dielectric Constant and Ionic Strength. Proteins. 41, 554-567 (2000).
• T. Fukamizo, A.H. Juffer, H.J. Vogel, Y. Honda, H. Tremblay, I. Boucher, W.A. Neugebauer and R. Brzezinski, Theoretical Calculation of pK_a Reveals an Important Role of Arg205 in the Activity and Stability of Streptomyces sp. N174 Chitosanase. J. Biol. Chem., 275, 25633-25640 (2000).
• A. Weljie, T. E. Clarke, A.H. Juffer, A.C. Harmon and H.J. Vogel, Comparative Modeling Studies of the Calmodulin-Like Domain of Calcium-Dependent Protein Kinase from Soybean. Proteins, 39, 343-357 (2000).