Andrzej Kolinski Research Group

Coarse-grained protein modeling

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Publications

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1998
Tertiary structure prediction of the KIX domain of CBP using Monte Carlo simulations driven by restraints derived from multiple sequence alignmentsOrtiz, A.R., Koliński, A. & Skolnick, J.Proteins 30, 287–294, 1998.
1997
Algorithm for rapid reconstruction of protein backbone from alpha carbon coordinatesMilik, M., Koliński, A. & Skolnick, J.Journal of Computational Chemistry 18, 80–85, 1997.
Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?Skolnick, J., Jaroszewski, L., Koliński, A. & Godzik, A.Protein Science 6, 676–688, 1997.
Determinants of secondary structure of polypeptide chains: Interplay between short range and burial interactionsKoliński, A. & Skolnick, J.Journal of Chemical Physics 107, 953–964, 1997.
High coordination lattice models of protein structure, dynamics and thermodynamicsKoliński, A. & Skolnick, J.Acta Biochim Polonica 44, 389–422, 1997.
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.
Method for low resolution prediction of small protein tertiary structureOrtiz, A.R., Hu, W.-P., Koliński, A. & Skolnick, J.Proceeding of II-nd Pacific Symposium on Biocomputing 316–327, 1997.
A method for the prediction of surface "U"-turns and transglobular connections in small proteinsKoliński, A., Skolnick, J., Godzik, A. & Hu, W.-P.Proteins 27, 290–308, 1997.
MONSSTER: a method for folding globular proteins with a small number of distance restraintsSkolnick, J., Koliński, A. & Ortiz, A.R.Journal of Molecular Biology 265, 217–241, 1997.
Monte Carlo lattice dynamics and the prediction of protein foldsSkolnick, J., Koliński, A., van Gunsteren, W.F., Weiner, P.K. & Wilkinson, A.J.Computer Simulations of Biomolecular Systems. Theoretical and Experimental Applications pp, 395–429, 1997.
1996
An algorithm for prediction of structural elements in small proteinsKoliński, A., Skolnick, J. & Godzik, A.Proceeding of I-st Pacific Symposium on Biocomputing 446–460, 1996.
Does a backwardly read protein sequence have a unique native state?Olszewski, K.A., Koliński, A. & Skolnick, J.Protein Engineering 9, 5–14, 1996.
Folding simulations and computer redesign of protein A three-helix bundle motifsOlszewski, K.A., Koliński, A. & Skolnick, J.Proteins 25, 286–299, 1996.
A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutantsVieth, M., Koliński, A., Brooks, III, C.L. & Skolnick, J.DIMACS Series in Discrete Mathematics and Theoretical Computer Science 23, 233–236, 1996.
Lattice models of protein folding. Dynamics and thermodynamicsKoliński, A. & Skolnick, J.Lattice models of protein folding. Dynamics and thermodynamics, Austin, TX, Chapman & Hall. (Chapman & Hall.: Austin, TX, 1996).
Method for predicting the state of association of discretized protein models. Application to leucine zippers.Vieth, M., Koliński, A. & Skolnick, J.Biochemistry 35, 955–967, 1996.
On the origin of the cooperativity of protein folding: implications from model simulationsKoliński, A., Galazka, W. & Skolnick, J.Proteins 26, 271–287, 1996.
Prediction of the quaternary structure of coiled coils: GCN4 leucine zipper and its mutants.Vieth, M. et al.Proceeding of I-st Pacific Symposium on Biocomputing 653–662, 1996.
1995
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.
Computer design of idealized beta-motifsKoliński, A., Galazka, W. & Skolnick, J.Journal of Chemical Physics 103, 10286–10297, 1995.
De novo simulations of the folding of GCN4 and its mutantsSkolnick, J., Vieth, M., Koliński, A. & Brooks, III, C.L.Modeling of Biomolecular Structures and Mechanisms 8, 95–98, 1995.
Neural network system for the evaluation of side-chain packing in protein structuresMilik, M., Koliński, A. & Skolnick, J.Protein Engineering 8, 225–236, 1995.
Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipperVieth, M., Koliński, A., Brooks, III, C.L. & Skolnick, J.Journal of Molecular Biology 251, 448–67, 1995.
A reduced model of short range interactions in polypeptide chainsKoliński, A., Milik, M., Rycombel, J. & Skolnick, J.Journal of Chemical Physics 103, 4312–4323, 1995.
A simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulationsVieth, M., Koliński, A. & Skolnick, J.Journal of Chemical Physics 102, 6189–6193, 1995.

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