"Making drug discovery a click"


2016
Jin Dai, Antti J Niemi, Jianfeng He, Adam Sieradzan, Nevena Ilieva,Bloch spin waves and emergent structure in protein folding with HIV envelope glycoprotein as an example, Phys. Rev. E 93, 032409 (2016)
Xubiao Peng, Adam Sieradzan, Antti J Niemi,Thermal unfolding of myoglobin in the Landau-Ginzburg-Wilson approach, arXiv:1602.02369 [q-bio.BM] (2016)
Theodora Ioannidoua and Antti J. Niemi,Poisson hierarchy of discrete strings, Physics Letters A 380, 3 (2016)
2015
Xubiao Peng, Jianfeng He, Antti J Niemi,Clustering and percolation in protein loop structures, BMC Structural Biology, 15:22 (2015)
N. Ilieva, J. Dai, A. Sieradzan, and A. Niemi,Solitons and protein folding: An In Silico experiment, AIP Conf. Proc. 1684, 030006 (2015)
A. Sinelnikova, A. J. Niemi, and M. Ulybyshev,Phase diagram and the pseudogap state in a linear chiral homopolymer model, Phys. Rev. E 92, 032602 (2015)
Ivan Gordeli, Dmitry Melnikov, Antti Niemi, Ara Sedrakyan,Chern-Simons Improved Hamiltonians for Strings in Three Space Dimensions, arXiv:1508.03268 [hep-th] (2015)
N Ilieva, A Niemi, X Peng, A Sieradzan,Kink Formation Dynamics in a Single alpha-helical Protein, Biomath Communications Vol 2, No 1 (2015)
Jianfeng He, Jin Dai, Nevena Ilieva, Antti Niemi,Structural Diversity of Amyloid Proteins in Intermediate States, Biomath Communications, Vol 2, No 1 (2015)
Jianfeng He, Jin Dai, Jing Li, Xubiao Peng, Antti J Niemi,Aspects of structural landscape of human islet amyloid polypeptide, J. Chem. Phys. 142, 045102 (2015)
Adam Liwo, Antti J. Niemi, Xubiao Peng, Adam K Sieradzan,A novel coarse-grained description of protein structure and folding by UNRES force field and Discrete Nonlinear Schrödinger Equation, Frontiers in Computational Chemistry. Vol. 1, Pp. 257-289 (2015)
2014
Andrey Krokhotin, Stam Nicolis, Antti J. Niemi,Long range correlations and folding angle with applications to α-helical proteins, J. Chem. Phys. 140, 095103 (2014)
Andrey Krokhotin, Adam Liwo, Gia Maisuradze, Antti Niemi, and Harold Scheraga,Kinks, loops and protein folding with protein A as an example, Journal of Chemical Physics, 140, 025101 (2014)
2013
M. Lundgren, Andrei Krokhotin, and Antti J. Niemi,Topology and structural self-organization in folded proteins, Phys. Rev. E 88, 042709 (2013)
K Hinsen, S Hu, GR Kneller, AJ Niemi,A comparison of reduced coordinate sets for describing protein structure, The Journal of Chemical Physics 139, 124115
Shuangwei Hu, Ying Jiang, and Antti J. Niemi,Energy functions for stringlike continuous curves, discrete chains, and space-filling one dimensional structures, Phys. Rev. D 87, 105011 (2013)
Andrey Krokhotin, Martin Lundgren, Antti J Niemi, Xubiao Peng, Soliton driven relaxation dynamics and protein collapse in the villin headpiece, Journal of Physics: Condensed Matter 25 (32), 325103
Andrey Krokhotin, Antti Niemi, and Xubiao Peng, On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics, J. Chem. Phys., 138, 175101 (2013)
2012
Andrey Krokhotin, Martin Lundgren, and Antti J. Niemi, Solitons and collapse in the λ−repressor protein, Phys. Rev. E 86, 021923 (2012)
Martin Lundgren, and Antti J. Niemi, Correlation between protein secondary structure, backbone bond angles, and side-chain orientations, Phys. Rev. E 86, 021904 (2012)
Andrey Krokhotin, Adam Liwo, Antti J. Niemi, and Harold A. Scheraga, Coexistence of Phases in a Protein Heterodimer, J. Chem. Phys. 137, 035101 (2012)
Lundgren, M,. Niemi, A.J., Sha, F., Protein loops, solitons, and side-chain visualization with applications to the left-handed helix region, Phys. Rev. E 85, 061909 (2012)
Andrei Krokhotin, Antti J. Niemi, and Xubiao Peng, Soliton concepts and protein structure, Phys. Rev. E 85, 031906 (2012)
2011
Martin Lundgren, Antti J. Niemi, Covalent bond symmetry breaking and protein secondary structure, arXiv:1109.0423
Shuangwei Hu, Martin Lundgren, and Antti J. Niemi, Discrete Frenet frame, inflection point solitons, and curve visualization with applications to folded proteins, Phys. Rev. E 83, 061908 (2011)
Andrey Krokhotin, Antti J. Niemi, The protein dynamical transition is a pseudogap changeover, arXiv:1109.4657
Shuangwei Hu, Andrei Krokhotin, Antti J. Niemi, and Xubiao Peng, Towards quantitative classification of folded proteins in terms of elementary functions, Phys. Rev. E 83, 041907 (2011)
Nora Molkenthin, Shuangwei Hu, and Antti J. Niemi, Discrete Nonlinear Schr�dinger Equation and Polygonal Solitons with Applications to Collapsed Proteins, Phys. Rev. Lett. 106, 078102 (2011)
M. N. Chernodub, Martin Lundgren, and Antti J. Niemi, Elastic energy and phase structure in a continuous spin Ising chain with applications to chiral homopolymers, Phys. Rev. E 83, 011126 (2011)
Andrei Krokhotine, Antti J. Niemi, Solitons and Physics of the Lysogenic to Lytic Transition in Enterobacteria Lambda Phage, arXiv:1104.2252
2010
Ulf H. Danielsson, Martin Lundgren1, and Antti J. Niemi, Gauge field theory of chirally folded homopolymers with applications to folded proteins, Phys. Rev. E 82, 021910 (2010)
Maxim Chernodub, Shuangwei Hu, and Antti J. Niemi, Topological solitons and folded proteins, Phys. Rev. E 82, 011916 (2010)
2009
Martin Lundgren, Antti J. Niemi, Knots and Swelling in Protein Folding, arXiv:0906.4950