Andrzej Kolinski Research Group

Coarse-grained protein modeling

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Publications

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Conference Proceedings
Application of a high coordination lattice model in protein structure predictionKoliński, A., Rotkiewicz, P. & Skolnick, J.Proceedings of HRLC Workshop pp, 100–130, 1998.
Journal Article
2-Ethyl and 2-ethylidene analogues of 1alpha,25-dihydroxy-19-norvitamin D(3): synthesis, conformational analysis, biological activities, and docking to the modeled rVDR ligand binding domain.Sicinski, R.R. et al.Journal of Medicinal Chemistry 45, 3366-80, 2002.
5-HT2 receptor affinity, docking studies and pharmacological evaluation of a series of 1,3-disubstituted thiourea derivativesBielenica, A. et al.European Journal of Medicinal Chemistry 116, 173–186, 2016.
Ab initio folding of proteins using restraints derived from evolutionary informationOrtiz, A.R., Koliński, A., Rotkiewicz, P., Ilkowski, B. & Skolnick, J.Proteins Suppl. 3, 177–185, 1999.
Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinementSkolnick, J. et al.Proteins 45, 149–156, 2001.
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.
Analysis and optimization of interactions between peptides mimicking the GD2 ganglioside and the monoclonal antibody 14G2aHorwacik, I. et al.International Journal of Molecular Medicine 28, 47–57, 2011.
Combining Structural Aggregation Propensity and Stability Predictions To Redesign Protein SolubilityGil-Garcia, M. et al.Molecular Pharmaceutics 15, 3846-3859, 2018.
Computational analysis of the active sites in binary and ternary complexes of the vitamin D receptorSicinska, W. & Rotkiewicz, P.The Journal of Steroid Biochemistry and Molecular Biology 103, 305-9, 2007.
Computer Modeling of Radiation-Induced in-Source Solid-State PolymerizationsOrszagh, A., Koliński, A. & Romiszowski, P.Polymer 20, 113, 1979.
Conservation of complex knotting and slipknotting patterns in proteins.Sulkowska, J.I., Rawdon, E.J., Millett, K.C., Onuchic, J.N. & Stasiak, A.Proceedings of the National Academy of Sciences of the United States of America 109, E1715-23, 2012.
Denatured proteins and early folding intermediates simulated in a reduced conformational spaceKmiecik, S., Kurcinski, M., Rutkowska, A., Gront, D. & Koliński, A.Acta Biochimica Polonica 53, 131–143, 2006.
Design and synthesis of novel 1H-tetrazol-5-amine based potent antimicrobial agents: DNA topoisomerase IV and gyrase affinity evaluation supported by molecular docking studiesSzulczyk, D. et al.European Journal of Medicinal Chemistry 156, 631 - 640, 2018.
DNA vaccine expressing the mimotope of GD2 ganglioside induces protective GD2 cross-reactive antibody responsesBolesta, E. et al.Cancer Research 65, 3410–8, 2005.
DNA vaccine expressing the mimotope of GD2 ganglioside induces protective GD2 cross-reactive antibody responsesBolesta, E. et al.Cancer Research 65, 3410–8, 2005.
Effect of double bonds on the dynamics of hydrocarbon chainsRey, A., Koliński, A., Skolnick, J. & Levine, Y.K.Journal of Chemical Physics 97, 1240–1249, 1992.
An efficient Monte Carlo model of protein chains. Modeling the short-range correlations between side group centers of massKoliński, A., Jaroszewski, L., Rotkiewicz, P. & Skolnick, J.The Journal of Physycal Chemistry B 102, 4628–4637, 1998.
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.
Identifying knots in proteins.Millett, K.C., Rawdon, E.J., Stasiak, A. & Sulkowska, J.I.Biochemical Society Transactions 41, 533-7, 2013.
Knot localization in proteins.Rawdon, E.J., Millett, K.C., Sulkowska, J.I. & Stasiak, A.Biochemical Society Transactions 41, 538-41, 2013.
KnotProt: a database of proteins with knots and slipknotsJamroz, M. et al.Nucleic Acids Research 43, D306-D314, 2015.
Knotting pathways in proteins.Sulkowska, J.I. et al.Biochemical Society Transactions 41, 523-7, 2013.
Knotting pathways in proteins.Sulkowska, J.I. et al.Biochemical Society Transactions 41, 523-7, 2013.
Mechanical unfolding of acylphosphatase studied by single-molecule force spectroscopy and MD simulationsArad-Haase, G. et al.Biophys J 99, 238-47, 2010.
A method for prediction of protein structure from sequenceSkolnick, J., Koliński, A., Brooks, III, C.L., Godzik, A. & Rey, A.Current Biology 3, 414–423, 1993.

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