1994
Godzik, A, Skolnick J. 1994. Flexible algorithm for direct multiple alignment of protein structures and sequences. Computer applications in the biosciences: CABIOS. 10(6):587-96. PDF
Vieth, M, Kolinski A, Brooks CL, Skolnick J. 1994. Prediction of the folding pathways and structure of the GCN4 leucine zipper. Journal of molecular biology. 237(4):361-7. PDF
Kolinski, A, Skolnick J. 1994. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins. 18(4):338-52. PDF
Kolinski, A, Skolnick J. 1994. Monte Carlo simulations of protein folding. II. Application to protein A, ROP, and crambin. Proteins. 18(4):353-66. PDF
Rey, A, Skolnick J. 1994. Computer simulation of the folding of coiled coils. The Journal of Chemical Physics. 100(3):2267. PDF
Baumgartner, A, Skolnick J. 1994. Polymer Electrophoresis across a Model Membrane. The Journal of Physical Chemistry. 98(41):10655-10658. PDF
Skolnick, J, Kolinski A. 1994. De novo prediction of protein tertiary structure. Polymer Preprints. 35:82-83. PDF
Sikorski, A, Kolinski A, Skolnick J. 1994. Dynamics of star branched polymers in a matrix of linear chains — a Monte Carlo study. Macromolecular Theory and Simulations. 3(4):715-729. PDF
1993
Godzik, A, Skolnick J, Kolinski A. 1993. Regularities in interaction patterns of globular proteins. Protein engineering. 6(8):801-10. PDF
Rey, A, Skolnick J. 1993. Computer modeling and folding of four-helix bundles. Proteins. 16(1):8-28. PDF
Skolnick, J, Kolinski A, Godzik A. 1993. From independent modules to molten globules: observations on the nature of protein folding intermediates. Proceedings of the National Academy of Sciences of the United States of America. 90(6):2099-100. PDF
Skolnick, J, Kolinski A, Brooks CL, Godzik A, Rey A. 1993. A method for predicting protein structure from sequence. Current biology: CB. 3(7):414-23. PDF
Milik, M, Skolnick J. 1993. Insertion of peptide chains into lipid membranes: an off-lattice Monte Carlo dynamics model. Proteins. 15(1):10-25. PDF
Godzik, A, Kolinski A, Skolnick J. 1993. De novo and inverse folding predictions of protein structure and dynamics. Journal of computer-aided molecular design. 7(4):397-438. PDF
Kolinski, A, Godzik A, Skolnick J. 1993. A general method for the prediction of the three dimensional structure and folding pathway of globular proteins: Application to designed helical proteins. The Journal of Chemical Physics. 98(9):7420. PDF
Levine, YK, Kolinski A, Skolnick J. 1993. A lattice dynamics study of a Langmuir monolayer of monounsaturated fatty acids. The Journal of Chemical Physics. 98(9):7581. PDF
Godzik, A, Kolinski A, Skolnick J. 1993. Lattice representations of globular proteins: How good are they? Journal of Computational Chemistry. 14(10):1194-1202. PDF
Kolinski, A, Skolnick J. 1993. Comment on “Local knot model of entangled polymer chains”. The Journal of Physical Chemistry. 97(13):3450-3450. PDF
Baginski, M, Piela L, Skolnick J. 1993. The ethylene group as a peptide bond mimicking unit: A theoretical conformational analysis. Journal of Computational Chemistry. 14(4):471-477. PDF
1992
Godzik, A, Kolinski A, Skolnick J. 1992. Topology fingerprint approach to the inverse protein folding problem. Journal of molecular biology. 227(1):227-38. PDF
Milik, M, Skolnick J. 1992. Spontaneous insertion of polypeptide chains into membranes: a Monte Carlo model. Proceedings of the National Academy of Sciences of the United States of America. 89(20):9391-5. PDF
Godzik, A, Skolnick J. 1992. Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination. Proceedings of the National Academy of Sciences of the United States of America. 89(24):12098-102. PDF
Godzik, A, Skolnick J, Kolinski A. 1992. Simulations of the folding pathway of triose phosphate isomerase-type alpha/beta barrel proteins. Proceedings of the National Academy of Sciences of the United States of America. 89(7):2629-33. PDF
Kolinski, A, Skolnick J. 1992. Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides. The Journal of Chemical Physics. 97(12):9412. PDF
Rey, A, Kolinski A, Skolnick J, Levine YK. 1992. Effect of double bonds on the dynamics of hydrocarbon chains. The Journal of Chemical Physics. 97(2):1240. PDF
Vieth, M, Koliński A, Skolnick J, Sikorski A. 1992. Prediction of protein secondary structure by neural networks: encoding short and long range patterns of amino acid packing. Acta biochimica Polonica. 39(4):369-92. PDF
Rey, A, Skolnick J. 1992. Efficient algorithm for the reconstruction of a protein backbone from the alpha-carbon coordinates. Journal of Computational Chemistry. 13(4):443-456. PDF
Milik, M, Skolnick J, Kolinski A. 1992. Monte Carlo studies of an idealized model of a lipid-water system. The Journal of Physical Chemistry. 96(10):4015-4022. PDF
Ngai, KL, Peng SL, Skolnick J. 1992. Generalized Fokker-Planck approach to the coupling model and comparison with computer simulations. Macromolecules. 25(8):2184-2191. PDF
1991
Skolnick, J, Kolinski A. 1991. Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics. Journal of molecular biology. 221(2):499-531. PDF
Levine, YK, Kolinski A, Skolnick J. 1991. Monte Carlo dynamics study of motions in cis-unsaturated hydrocarbon chains. The Journal of Chemical Physics. 95(5):3826. PDF
Kolinski, A, Milik M, Skolnick J. 1991. Static and dynamic properties of a new lattice model of polypeptide chains. The Journal of Chemical Physics. 94(5):3978. PDF
Rey, A, Skolnick J. 1991. Comparison of lattice Monte Carlo dynamics and Brownian dynamics folding pathways of α-helical hairpins. Chemical Physics. 158(2-3):199-219. PDF
Ngai, KL, Skolnick J. 1991. Correspondence between the coupling model predictions and computer simulations: diffusion of a probe polymer in a matrix having different degrees of polymerization. Macromolecules. 24(7):1561-1566. PDF
1990
Sikorski, A, Skolnick J. 1990. Dynamic Monte Carlo simulations of globular protein folding. Model studies of in vivo assembly of four helix bundles and four member beta-barrels. Journal of molecular biology. 215(1):183-98. PDF
Skolnick, J, Kolinski A. 1990. Simulations of the folding of a globular protein. Science. 250(4984):1121-5. PDF
Skolnick, J, Kolinski A. 1990. Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. I. Six-member, Greek key beta-barrel proteins. Journal of molecular biology. 212(4):787-817. PDF
Sikorski, A, Skolnick J. 1990. Dynamic Monte Carlo simulations of globular protein folding/unfolding pathways. II. Alpha-helical motifs. Journal of molecular biology. 212(4):819-36. PDF
Milik, M, Kolinski A, Skolnick J. 1990. Monte Carlo dynamics of a dense system of chain molecules constrained to lie near an interface. A simplified membrane model. The Journal of Chemical Physics. 93(6):4440-6. PDF
Holtzer, A, Holtzer M E, Skolnick J. 1990. Does the unfolding transition of two-chain, coiled coil proteins involve a continuum of intermediates? The Protein Folding Problem. AAAS Seminar Volume
Skolnick, J, Kolinski A, Sikorski A. 1990. Dynamic Monte Carlo simulations of globular protein and structure. Chemical Design Automation News . 5:1-20. PDF
Skolnick, J, Kolinski A. 1990. Dynamics of dense polymer systems: Computer simulations and analytic theories. Advances in Chemical Physics . 77:223-278. PDF
1989
Skolnick, J, Kolinski A, Yaris R. 1989. Monte Carlo studies on equilibrium globular protein folding. II. Beta-barrel globular protein models. Biopolymers. 28(6):1059-95. PDF
Sikorski, A, Skolnick J. 1989. Monte Carlo studies on equilibrium globular protein folding. III. The four helix bundle. Biopolymers. 28(6):1097-113. PDF
Skolnick, J, Kolinski A, Yaris R. 1989. Dynamic Monte Carlo study of the folding of a six-stranded Greek key globular protein. Proceedings of the National Academy of Sciences of the United States of America. 86(4):1229-33. PDF
Sikorski, A, Skolnick J. 1989. Monte Carlo simulation of equilibrium globular protein folding: alpha-helical bundles with long loops. Proceedings of the National Academy of Sciences of the United States of America. 86(8):2668-72. PDF
Skolnick, J, Kolinski A. 1989. Computer simulations of globular protein folding and tertiary structure. Annual review of physical chemistry. 40:207-35. PDF
Skolnick, J, Kolinski A, Sikorski A, Yaris R. 1989. Dynamic Monte Carlo simulation of a melt of ring polymers. Polymer Preprints . 30:70-73. PDF
Skolnick, J. 1989. Dynamics of dense polymer systems. Dynamic Monte Carlo simulation results and analytic theory. In: Reactive and Flexible Molecules Liquids. Dorfmuller, T., ed., Klumer Academic Publishers 291:199-220. PDF
Yeates, AT, Skolnick J, Yaris R. 1989. Fit of a nonreptative model of polymer melt dynamics to experimental melt diffusion constant measurements. Journal of Polymer Science Part B: Polymer Physics. 27(1):151-154. PDF
Skolnick, J, Yaris R, Kolinski A. 1989. Phenomenological theory of polymer melt dynamics. International Journal of Modern Physics B. 3(1):33. PDF