Publications
Reprints or preprints available upon request. Email yiannis@cems.umn.edu
Supplementary Material for Publications
44) Kaznessis YN. "Models for synthetic biology." BMC Syst Biol. 2007 Nov 6;1(1):47, link
43) V. Sotiropoulos, YN. Kaznessis "An Adaptive Time Step Scheme for a System of SDE’s with Multiple Multiplicative Noise. Chemical Langevin Equation, a proof of concept", J. Chem. Phys. in press.
42) Reddy BV, Kaznessis YN. "Use of secondary structural information and C alpha-C alpha distance restraints to model protein structures with MODELLER." J Biosci. 2007 Aug;32(5):929-36.
41) D. Bolintineanu, A. Langham, T.H. Davis, Y. Kaznessis, "Molecular dynamics simulations of three protegrin-type anti-microbial peptides: interplay between charges at the termini, beta-sheet structure and amphiphilic interactions", Molecular Simulation, 2007, in press.
40) A. Langham, A.J. Waring, Y. Kaznessis, "Comparison of interactions between beta-hairpin decapeptides and SDS/DPC micelles from experimental and simulation data", BMC Biochemistry. 2007 Jul 16;8(1):11. link
39) S. Vicatos, Y. Kaznessis, "Separating true positive predicted residue contacts from false positive ones in mainly alpha proteins, using constrained Metropolis MC simulations." Proteins, 2007 .
38) C. Mulakala, J.D. Lambris, Y. Kaznessis, "A simple, yet highly accurate, QSAR model captures the complement inhibitory activity of compstatin", Bioorg Med Chem. 2007 Feb 15;15(4):1638-44, link.
37) H. Khandelia, Y. Kaznessis, "Structure of the Antimicrobial beta-hairpin Peptide Protegrin-1 in a DLPC Lipid Bilayer Investigated by Molecular Dynamics Simulation", BBA Biomembranes, 2007, 1768(3):509-20, link.
36) H. Khandelia, Y. Kaznessis, "Cation-π Interactions Stabilize the Structure of the Antimicrobial Peptide Indolicidin near Membranes: Molecular Dynamics Simulations", J. Phys. Chem. B, 2007, 111(1):242-250, link.
35) V. Sotiropoulos, Y. Kaznessis, "Computer-aided design of synthetic tetracycline-inducible regulatory networks", BMC Systems Biology, 2007, 1:7, link
34) H. Salis, Y. Kaznessis, "Using scaffold proteins to design gene-activating binary and ternary biological AND gates", 2006, 3(4):295-310, Physical Biology, link.
33) A. Langham, Y. Kaznessis "Effects of mutations on the C-terminus of protegrin-1: a molecular dynamics simulation study", Molecular Simulation, 2006, 32(3-4):193-201. link
32) J. Tomshine, Y. Kaznessis, "Optimization of a stochastically-simulated gene network model via simulated annealing." Biophysical Journal, 2006, 91(9):3196-205, link.
31) W. Wang, C. Mulakala, S.C. Ward, G. Jung, H. Luong, D. Pham , A.J. Waring, Y. Kaznessis, W. Lu, K.A. Bradley, R.I. Lehrer. "Retrocyclins kill bacilli and germinating spores of Bacillus anthracis and inactivate anthrax lethal toxin." Journal of Biological Chemistry, 2006, 281(43):32755-64. link
30) H. Khandelia, A.Langham, Y. Kaznessis, "Driving engineering of novel antimicrobial peptides from simulations of peptide-micelle interactions", BBA, 2006, 1758(9):1224-34, link
29) Y. Duan, B. Reddy, Y. Kaznessis "Residue conservation information for generating near-native structures in protein-protein docking" Journal of Bioinformatics and Computational Biology, 2006, 4:793-806, link
28) H. Khandelia, Y. Kaznessis, "Molecular Dynamics Investigation of the Influence of Anionic and Zwitterionic Interfaces on Antimicrobial Peptides' Structure: Implications on Peptide Toxicity and Activity" Peptides, 2006, 27(6):1192-1200. link
27) H. Salis, V. Sotiropoulos, Y. Kaznessis, "Multiscale Hy3S: Hybrid stochastic simulation for supercomputers" BMC Bioinformatics, 2006, 7:93. link
26) H. Salis, Y. Kaznessis, "An equation-free probabilistic steady state approximation: Dynamic application to the stochastic simulation of biochemical reaction networks" Journal of Chemical Physical, 2005, 123 (21): Art. No. 214106. link
25) L. Tuttle, H. Salis, J. Tomshine, Y. Kaznessis, "Model-driven design principles of gene networks: the oscillator" Biophysical Journal, 2005, 89 (6): 3873-3883. link
24) A. Langham, H. Khandelia, Y. Kaznessis, "How can protegrin-1 be both a potent antimicrobial and harmfully toxic?: Molecular dynamics simulations of a beta-sheet antimicrobial peptide in micelles" Biopolymers: Peptide Science, 2006, 84 (2): 219-231. link
23) Y. Kaznessis, “Multi-scale models for gene network engineering” Chemical Engineering Science, 2006, 61 (3): 940-953. link
22) Y. Kaznessis, "A review of methods in computational prediction of blood-brain partitioning" Current Medicinal Chemistry, Central Nervous System Agents, 2005, 5, (3): 185-191 link
21) H. Khandelia, Y. Kaznessis, "Molecular dynamics simulations of helical antimicrobial peptides in SDS micelles: What do point mutations achieve?" Peptides, 2005, 26 (11): 2037-2049. link.
20) V. Reddy, Y. Kaznessis, "Quantitative analysis of interfacial amino acid conservation in protein-protein hetero complexes" Journal of Bioinformatics and Computational Biology, 2005, 3(5):1137-50. link
19) H. Khandelia, Y. Kaznessis, "Molecular dynamics simulations of the helical antimicrobial peptide ovispirin-1 in zwitterionic dodecylphoshocholine micelles: Insights into host-cell toxicity" Journal of Physical Chemistry B, 2005; 109(26) pp 12990 - 12996 link.
18) Y. Duan, V. Reddy, Y. Kaznessis, "Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions" Protein Science, 2005 Feb; 14 (2): 316-328. link
17) H. Salis, Y. Kaznessis, "Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions" Journal of Chemical Physics, 122, 054103 (2005). link
16) H. Salis, Y. Kaznessis, "Numerical simulation of stochastic gene circuits" Computers & Chemical Engineering, Vol 29(3), 2005, p. 577-588. link
15) S. Vicatos, V.B. Reddy, Y. Kaznessis, "Prediction of distant residue contacts with the use of evolutionary information" Proteins, Bioinformatics, Structure and Genetics, 2005 Mar 1; 58 (4): 935-49. link
14) A. Langham, Y. Kaznessis, "Molecular dynamics simulations of the N-terminus of HIV GP-41 fusion peptide in SDS micelles" Journal of Peptide Science, 2005 Feb; 14( 2): 316-328. link
13) N. Ostberg , H. Khandelia, Y. Kaznessis, “Protegrin structure activity relationships: Using homology models of synthetic sequences to determine structural characteristics important for activity” Peptides, Vol. 26(2), p. 297-306, 2005. link
12) H. Wei, Y. Kaznessis, ‘Inferring gene regulatory relationships by combining target-target pattern recognition and regulator-specific motif examination” Biotechnology and Bioengineering, Vol. 89(1), p. 52-77, 2005. link
11) L.M. Gordon, P.W. Mobley, W. Lee, S. Eskandari, Y. Kaznessis, M.A. Sherman, A.J. Waring, "Conformational mapping of the N-terminal peptide of HIV-1 GP41 in lipid detergent and aqueous environments using 13C-enhanced Fourier transform infrared spectroscopy" Protein Science, Vol. 13, p. 1012-30, 2004. link
10) Y. N. Kaznessis, R.G. Larson, “Molecular mechanics simulations and bioinformatics calculations in the study of lung surfactants.” Invited chapter in the book “Recent Research Developments in Lung Surfactant and its Dysfunction” Edited by Kaushik Nag, Marcel-Dekker, 2005
9) Y. N. Kaznessis, S. Kim, R. G. Larson, “Specific mode of interaction between components of model pulmonary surfactants using computer simulations” Journal of Molecular Biology. Vol. 322, p. 569-582, 2002. PDF
8) Y. N. Kaznessis, S. Kim, R. G. Larson, “Simulations of zwitterionic and anionic phospholipid monolayers” Biophysical Journal, Vol. 82, 2002, p. 1731-42. PDF
7) Y. N. Kaznessis, M. E. Snow, C. J. Blankley, “Prediction of blood-brain partitioning using Monte Carlo simulations of molecules in water” Vol. 15, p. 697, 2001, Journal of Computer-Aided Molecular Design. PDF
6) Y. N. Kaznessis, L. Narashimhan, M. E. Snow, “Binding free energy calculations for Benzamidine-Trypsin complexes” Proceedings of Foundations of Molecular Modeling and Simulation Conference, AIChE Symposium Series, p. 283, 2000.
5) Y. N. Kaznessis, D. A. Hill, E. J. Maginn, “Dielectric relaxation of concentrated polymer solutions via molecular dynamics simulations” Journal of Chemical Physics, Vol. 111, p. 1325, 1999. PDF
4) Y. N. Kaznessis, D. A. Hill, E. J. Maginn, “Concentration and size dependence of dielectric strength and dielectric relaxation of flexible polymers in dilute and semidilute solutions of a theta solvent” Macromolecules, Vol. 32, p. 1284, 1999. PDF
3) Y. N. Kaznessis, D. A. Hill, E. J. Maginn, “Dielectric relaxation of dipole-inverted macromolecules using computer simulations” Macromolecules, Vol. 32, p. 6679, 1999. PDF
2) Y. N. Kaznessis, D. A. Hill, E. J. Maginn, “A molecular dynamics study of macromolecules in good solvents. Comparison with dielectric spectroscopy experiments” Journal of Chemical Physics, Vol. 109, p. 5078, 1998. PDF
1) Y. N. Kaznessis, D. A. Hill, E. J. Maginn, “Molecular dynamics simulations of polar polymer brushes" Macromolecules, Vol. 31, p. 3116, 1998. PDF
