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Coarse-grained protein modeling

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B
Protein fragment reconstruction using various modeling techniquesBoniecki, M., Rotkiewicz, P., Skolnick, J. & Koliński, A.Journal of Computer-Aided Molecular Design 17, 725–38, 2003.
C
Thermal unfolding of proteins.Cieplak, M. & Sulkowska, J.I.J Chem Phys 123, 194908, 2005.
E
Protein modeling with reduced representation: statistical potentials and protein folding mechanismEkonomiuk, D., Kielbasinski, M. & Koliński, A.Acta Biochimica Polonica 52, 741–8, 2005.
F
Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution modelsFeig, M., Rotkiewicz, P., Koliński, A., Skolnick, J. & Brooks, III, C.L.Proteins 41, 86–97, 2000.
G
Multibody coarse-grained potentials for native structure recognition and quality assessment of protein modelsGniewek, P., Leelananda, S.P., Koliński, A., Jernigan, R.L. & Kloczkowski, A.Proteins 79, 1923–9, 2011.
Are proteins ideal mixtures of amino acids? Analysis of energy parameter setsGodzik, A., Koliński, A. & Skolnick, J.Protein Science: a Publication of the Protein Society 4, 2107–2117, 1995.
BioShell–a package of tools for structural biology computationsGront, D. & Koliński, A.Bioinformatics (Oxford, England) 22, 621–622, 2006.
Backbone building from quadrilaterals: a fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinatesGront, D., Kmiecik, S. & Koliński, A.Journal of Computational Chemistry 28, 1593–7, 2007.
Fast and accurate methods for predicting short-range constraints in protein modelsGront, D. & Koliński, A.Journal of Computer-Aided Molecular Design 22, 783–8, 2008.
HCPM–program for hierarchical clustering of protein modelsGront, D. & Koliński, A.Bioinformatics 21, 3179–80, 2005.
A new approach to prediction of short-range conformational propensities in proteinsGront, D. & Koliński, A.Bioinformatics (Oxford, England) 21, 981–987, 2005.
T-Pile–a package for thermodynamic calculations for biomoleculesGront, D. & Koliński, A.Bioinformatics (Oxford, England) 23, 1840–1842, 2007.
H
Improved method for prediction of protein backbone U-turn positions and major secondary structural elements between U-turnsHu, W.-P., Koliński, A. & Skolnick, J.Proteins 29, 443–460, 1997.
J
Modeling of loops in proteins: a multi-method approachJamroz, M. & Koliński, A.BMC Structural Biology 10, 5, 2010.
K
AAindex: amino acid index database, progress report 2008Kawashima, S. et al.Nucleic Acids Research 36, D202–5, 2008.
Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genomeKihara, D., Zhang, Y., Lu, H., Koliński, A. & Skolnick, J.Proceedings of the National Academy of Sciences of the United States of America 99, 5993–5998, 2002.
TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraintsKihara, D., Lu, H., Koliński, A. & Skolnick, J.Proceedings of the National Academy of Sciences of the United States of America 98, 10125–30, 2001.
Distance matrix-based approach to protein structure predictionKloczkowski, A. et al.Journal of Structural and Functional Genomics 10, 67–81, 2009.
Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force fieldKmiecik, S., Gront, D. & Koliński, A.BMC Structural Biology 7, 43, 2007.
Characterization of protein-folding pathways by reduced-space modelingKmiecik, S. & Koliński, A.Proceedings of the National Academy of Sciences of the United States of America 104, 12330–5, 2007.
Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptidesKoliński, A. & Skolnick, J.Journal of Chemical Physics 97, 9412–9426, 1992.
Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinementKoliński, A., Betancourt, M., Kihara, D., Rotkiewicz, P. & Skolnick, J.Proteins 44, 133–149, 2001.
Unfolding of globular proteins: monte carlo dynamics of a realistic reduced modelKoliński, A., Klein, P., Romiszowski, P. & Skolnick, J.Biophysical Journal 85, 3271–3278, 2003.
A simple lattice model that exhibits a protein-like cooperative all-or-none folding transitionKoliński, A., Gront, D., Pokarowski, P. & Skolnick, J.Biopolymers 69, 399–405, 2003.
Protein modeling and structure prediction with a reduced representationKoliński, A.Acta Biochimica Polonica 51, 349–71, 2004.

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