1995
Godzik, A, Koliński A, Skolnick J. 1995. Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets Protein science : a publication of the Protein Society. 4(10):2107-17. PDF
Milik, M, Skolnick J. 1995. A Monte Carlo model of fd and Pf1 coat proteins in lipid membranes. Biophysical journal. 69(4):1382-6. PDF
Baumgärtner, A, Skolnick J. 1995. Spontaneous translocation of a polymer across a curved membrane. Physical review letters. 74(11):2142-2145. PDF
Milik, M, Kolinski A, Skolnick J. 1995. Neural network system for the evaluation of side-chain packing in protein structures. Protein engineering. 8(3):225-36. PDF
Vieth, M, Kolinski A, Brooks CL, Skolnick J. 1995. Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper. Journal of molecular biology. 251(3):448-67. PDF
Kolinski, A, Galazka W, Skolnick J. 1995. Computer design of idealized β-motifs. The Journal of Chemical Physics. 103(23):10286. PDF
Kolinski, A, Milik M, Rycombel J, Skolnick J. 1995. A reduced model of short range interactions in polypeptide chains. The Journal of Chemical Physics. 103(10):4312. PDF
Vieth, M, Kolinski A, Skolnick J. 1995. A simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulations. The Journal of Chemical Physics. 102(15):6189.
Vieth, M, Kolinski A, Brooks III C, Skolnick J. 1995. Prediction of Quaternary Structure of Coiled Coils. Application to Mutants of the GCN4 Leucine Zipper. Journal of Molecular Biology. 251(3):448-467. PDF
Skolnick, J, Vieth M, Kolinski A, Brooks CL. 1995. De novo simulations of the folding of GCN4 and its mutants. In: Modeling of Biomolecular Structures and Mechanisms. A. Pullman, et al., Eds., Kluwer Acad./Netherlands8:95-98. PDF
Milik, M, Skolnick J. 1995. An object oriented environment for artificial evolution of protein sequences: The example of rational design of transmembrane sequences. Evolutionary Conference. PDF
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