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Book Chapter
Roterman, I, Brylinski M, Konieczny L.  2009.  Active site recognition in silico. Structure-function relation in proteins. 1:105-127.
Kolinski, A, Godzik A, Skolnick J.  1999.  Contact Maps. Encyclopedia of Molecular Biology. :567-571. PDF
Skolnick, J, Vieth M, Kolinski A, Brooks CL.  1995.  De novo simulations of the folding of GCN4 and its mutants. Modeling of Biomolecular Structures and Mechanisms. 8:95-98. PDF
Roterman, I, Brylinski M, Konieczny L, Jurkowski W.  2007.  Early-stage protein folding - In silico model. Recent Advances in Structural Bioinformatics. 1:69-104. PDF
Roterman, I, Konieczny L, Brylinski M.  2009.  Folding process in the presence of specific ligand. Structure-function relation in proteins. 1:129-148.
Mukherjee, S, Szilágyi A, Roy A, Zhang Y.  2010.  Genome-wide protein structure prediction . Multiscale approaches to protein modeling: structure prediction, dynamics, thermodynamics and macromolecular assemblies. :255-280.
Roterman, I, Konieczny L, Brylinski M.  2009.  Late-stage folding intermediate in silico model. Structure-function relation in proteins. 1:79-103.
Kolinski, A, Skolnick J.  1996.  Lattice Models of Protein Folding. Dynamics and Thermodynamics. :202.
Skolnick, J, Milik M.  1997.  Modeling of Membrane Proteins and Peptides. Membrane Proteins Assembly, Part IV. :201-220. PDF
Skolnick, J, Kolinski A.  1998.  Monte Carlo approaches to the protein folding problem. Monte Carlo Methods in Chemical Physics. 105:203-242. PDF
Skolnick, J, Kolinski A.  1997.  Monte Carlo Lattice Dynamics and the Prediction of Protein Folds. Computer Simulations of Biomolecular Systems. 3:395-429. PDF
Skolnick, J.  1982.  An order-disorder theory of stress-strain behavior of glassy polymers. Static and Dynamic Properties of the Polymeric Solid State.
Skolnick, J, Kolinski A.  1998.  Protein Modeling. Encyclopedia of Computational Chemistry. :2200-2211.
Pandit, S B, Zhou H, Skolnick J.  2010.  TASSER-based protein structure prediction. Introduction to Protein Structure Prediction: Methods and Algorithms. 14:219-242. PDF
Conference Paper
Guan, W, Ozakin A, Gray A, Borreguero J, Pandit S, Jagielska A, Wroblewska L, Skolnick J.  2011.  Learning Protein Folding Energy Functions. 2011 IEEE 11th International Conference on Data Mining (ICDM)2011 IEEE 11th International Conference on Data Mining. :1062-1067. PDF
YAMATO, ICHIRO, Ando T, SUZUKI AYUMI, HARADA KAZUO, ITOH SEIGO.  2008.  QP-PQ: Quantum Probability and White Noise Analysis TOWARD IN SILICO BIOLOGY (FROM SEQUENCES TO SYSTEMS). Quantum Bio-Informatics - From Quantum Information to Bio-InformaticsQuantum Bio-Informatics - From Quantum Information to Bio-Informatics. :440-455.
Conference Proceedings
Kolinski, A, Rotkiewicz P, Skolnick J.  1998.  Application of a high coordination lattice model in protein structure prediction. Workshop on Monte Carlo Approach to Biopolymers and Protein Folding. :377-388. PDF
Kolinski, A, Skolnick J, Yaris R.  1985.  Monte Carlo dynamics of diamond-lattice multichain systems. La Jolla Workshop on Polymer Flow Interaction. 137:241-245. PDF
Skolnick, J, Brylinski M.  2009.  Novel computational approaches to drug discovery. Proceedings of the International Conference of the Quantum Bio-Informatics III. PDF
Skolnick, J, Fetrow JS, Ortiz AR, Kolinski A.  1999.  The role of computational biology in the genomics revolution. National Research Council’s Chemical Sciences Roundtable Workshop on the Impact of Advances in Computing and Communications Technologies on Chemical Sciences and Technology. PDF
Reva, BA, Finkelstein AV, Skolnick J.  1998.  A self-consistent field optimization approach to build energetically and geometrically correct lattice models of proteins. Annual International Conference on Research in Computational Molecular Biology (RECOMB98) . :214-220. PDF
Journal Article