Andrzej Kloczkowski Publications

Adjunct Professor
Computational molecular biology
Structural bioinformatics
Prediction of protein structure, function and dynamics
Biomolecular simulations

Selected Publications
Sulkowska, J.I., Kloczkowski, A., Sen, T. Z., Cieplak M. and Jernigan, R.L., Prediction of the Order of Breaking Contacts during Protein Stretching, Proteins: Struct. Funct. Bioinf., 2007, in press.

Sen, T. Z., Kloster, M., Jernigan, R. L., Kolinski, A., Bujnicki, J., and Kloczkowski, A., Structure Prediction and Normal Mode Analysis of the Outer Membrane Transporter FecA,   Biophysical Journal, 2007, in press.

Cheng, H., Sen, T.Z., Jernigan, R.L., and Kloczkowski, A., Consensus Data Mining (CDM) Secondary Structure Prediction Server: Combining GOR V and Fragment Data Mining (FDM), Bioinformatics, 23, 2628-2630, 2007.

Pokarowski, P., Kloczkowski, A., Nowakowski, S., Pokarowska, M., Jernigan, R.L. and Kolinski, A. Ideal Amino Acid Exchange Forms Approximate Substitution Matrices, Proteins: Struct. Funct. Bioinf., 69, 379-393, 2007.
  
Feng, Y., Kloczkowski, A., and Jernigan, R. L., Four-Body Contact Potentials Derived from Two Protein Databases to Discriminate Native Structures from Decoys, Proteins: Struct. Funct. Bioinf., 68, 57-66, 2007.

Peto, M., Kloczkowski, A., and Jernigan, R.L., Shape-dependent designability studies of lattice proteins. Journal of Physics: Condensed Matter, 19, Art. No. 285220 (11pp), 2007.

Peto, M., Sen, T.Z., Jernigan, R.L. and Kloczkowski, A, Generation and enumeration of compact conformations on the 2D triangular and 3D fcc lattices, Journal of Chemical Physics, 127: Art. No. 044101 (10pp), 2007.

Mark, J.E., Abou-Hussein, R., Sen, T.Z,, and Kloczkowski, A., Monte Carlo Simulations on Nanoparticles in Elastomers. Effects of the Particles on the Dimensions of the Polymer Chains and the Mechanical Properties of the Networks, Macromolecular Symposia, 256, 40-47, 2007.

Yan, A., Kloczkowski, A., Hofmann, H., and Jernigan, R.L., Prediction of side chain orientations in          proteins by statistical machine learning methods, Journal of Biomolecular Structure and Dynamics, 25, 275-288, 2007.

Kloczkowski, A. and Kolinski, A., Theoretical Models and Simulations for Polymer Chains, In: Physical Properties of Polymers Handbook, 2nd Edition, Springer Verlag, New York, 2007, pp 67-81.

Kloczkowski, A. and Sen, T.Z.:  Magnetic, Piezoelectric, Pyroelectric and Ferroelectric Properties of Synthetic and Biological Polymers, In:  Physical Properties of Polymers Handbook, 2nd Edition, Springer Verlag, New York, 2007, pp 787-794.

Plewczynski, D., Tkacz, A., Wyrwicz, L.S., Godzik, A., Kloczkowski, A. and Rychlewski,            L., Support Vector Machine Classification of Linear Functional Motifs in Proteins, Journal of Molecular Modeling, 12, 453-461, 2006.

Sharaf, M.A., Kloczkowski, A., Sen, T.Z., Jacob, K.I. and Mark, J.E., Filler Induced Deformations of Amorphous Polyethylene Chains. The Effects of the Deformations on Elastomeric Properties and Some Comparisons with Experiments, European Polymer Journal, 42, 796-806, 2006.

Sharaf, M.A., Kloczkowski, A., Sen, T.Z., Jacob, K.I. and Mark, J.E, Molecular Modeling of  Matrix Chain Deformation in Nanofiber Filled Composites, Colloid & Polymer Science, 284, 700-709, 2006.

Sen, T. Z., Feng, Y., Garcia, J., Kloczkowski A., and Jernigan, R. L., The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models, Journal of Chemical Theory and Computation, 2, 696-704, 2006.

Sen, T. Z., Kloczkowski, and Jernigan, R. L., Functional Clustering of Yeast Proteins,  BMC Bioinformatics, 7, Art. No. 355, 2006.

Sen, T. Z., Kloczkowski, and Jernigan, R. L., A DNA-centric look at protein-DNA complexes, Structure, 14, 1341-1344, 2006.

Sen, T.Z., Cheng, H., Kloczkowski, A., and Jernigan, R.L, The Consensus Data Mining secondary structure prediction method by combining GOR V and Fragments Database Mining, Protein Science, 15, 2499-2506, 2006.

Jernigan, R.L. and Kloczkowski, A., Packing Regularities in Biological Structures Relate to Their Dynamics, In: Methods in Molecular Biology, Vol 350, Protein Folding Protocols, Y.        Bai and R. Nussinov (Eds), Humana Press, Totowa, NJ, 2006, pp. 251-276.

Pokarowski, P., Kloczkowski, A., Kothari, N., Pokarowska, M., Jernigan, R.L. and Kolinski, A. Inferring Ideal Amino Acid Interaction Forms from Statistical Protein Contact Potentials, Proteins: Struct. Funct. Bioinf., 59, 49-57, 2005.

Fernandez A., Tawfik, D.S., Berkhout, B., Sanders, R.W., Kloczkowski, A., Sen, T.Z and Jernigan R.L., Protein promiscuity: Drug resistance and native functions - HIV-1 case,  J. Biomol. Struct. Dyn., 22, 615-624, 2005.

Cheng, H., Sen, T.Z., Kloczkowski, A., Margaritis, D. and Jernigan, R.L., Prediction of Protein Secondary Structure by Mining Fragments Database, Polymer, 46, 4314-4321, 2005.

Kloczkowski, A., Sen, T.Z, and Sharaf M.A., The Largest Eigenvalue Method For Stereo Regular Vinyl Chains, Polymer, 46, 4373-4383, 2005.

Sen, T.Z., Jernigan, R.L., Garnier J., and Kloczkowski, A GOR V Server for Protein Secondary Structure Prediction, Bioinformatics, 21, 2787-27-88, 2005.

Plewczynski, D., Jaroszewski, L., Godzik, A., Kloczkowski, A., and Rychlewski, L Molecular Modeling of Phosphorylation Sites in Proteins using Database of Local Structure Segments, Journal of Molecular Modeling, 11, 431-438, 2005.

Sen, T.Z, and Sharaf M.A., Mark, J.E., and Kloczkowski, A., Modeling the Elastomeric Properties of Stereo-Regular Polypropylenes in Nanocomposites with Spherical Fillers, Polymer, 46, 7301-7308, 2005.

Mark, J. E., Abou-Hussein, R., Sen, T.Z., and Kloczkowski, A., Some Simulations on Filler  Reinforcement in Polymers, Polymer, 46, 8894-8904, 2005.

Kloczkowski, A., Sen, T.Z. and Jernigan, R.L.: The transfer matrix method for lattice proteins - an application with cooperative interactions, Polymer, 45, 707-716, 2004

Kloczkowski, A., Jernigan, R.L: Protein Conformational Computations-special issue of Polymer (Editorial), Polymer, 45, 507-507, 2004

Sen, T.Z., Kloczkowski, A., Jernigan, R.L., Yan, C., Honavar, V., Ho, K.-M., Wang, C.Z., Ihm, Y., Cao, H., Gu, X., Dobbs, D.L., Predicting Binding Sites of Protease-Inhibitor Complexes By Combining Several Methods, BMC Bioinformatics, 5, Art. No. 205, 2004.

Bagci, Z., Kloczkowski, A., Jernigan, R.L. and Bahar, I.: The origin and extent of coarse-grained regularities in protein internal packing, Proteins: Struct. Funct. Gen., 53, 56-67, 2003.

Kloczkowski, A., Ting, K-L., Jernigan, R.L. and Garnier, J.: Protein Secondary Structure Prediction Based on the GOR Algorithm with Multiple Sequence Alignments, Polymer, 43, 441-449, 2002.

Kloczkowski, A.:  Application of Statistical Mechanics to the Analysis of Various Physical Properties of Elastomeric Networks - A Review, Polymer, 43, 1503-1521, 2002

Kloczkowski, A, Erman B. and Mark, J.E.: Effect of Non-Gaussian Chains on Fluctuations of Junctions in Bimodal Networks, Polymer, 43, 2569-2574, 2002

Kloczkowski, A., Ting, K-L., Jernigan, R.L. and Garnier, J.: Combining the GOR V Algorithm with Evolutionary Information for Protein Secondary Structure Prediction from Amino Acid Sequence, Proteins: Struct. Funct. Gen., 49, 154-166, 2002.

Kloczkowski, A. and Jernigan, R.L., Loop Folds in Proteins and Evolutionary Conservation of Folding Nuclei, J. Biomol. Struct. Dyn., 20, 323-325, 2002.