Publications
1. Pillardy, J.; Olszewski, K.A.; Piela, L.; “Performance of the Shift Method of Global Minimization in Searches for Optimum Structures of Clusters of Lennard-Jones Atoms”, J. Phys. Chem. 1992, 96, 4337-4341.
2. Pillardy, J.; Olszewski, K.A.; Piela, L.; “Theoretically Predicted Lowest-Energy Structures of Water Clusters”, J. Mol. Struct. (Theochem), 1992, 270, 277-285.
3. Piela, L.; Olszewski, K.A.; Pillardy, J.; “On the Stability of Conformers”, J. Mol. Struct. (Theochem), 1994, 308, 229-239.
4. Pillardy, J.; Piela, L.; “Molecular Dynamics on Deformed Potential Energy Hypersurfaces”, J. Phys. Chem. 1995, 99, 11805-11812.
5. Pillardy, J.; Piela, L.; “Smoothing Techniques of Global Optimization. The Distance Scaling Method in Searches for the Most Stable Lennard-Jones Atomic Clusters” J. Comp. Chem., 1997, 18, page 2040-2049.
6. Pillardy, J.; Piela, L.; “Multiple Elliptical-Gaussian-Density Annealing as a Tool for Finding the Most Stable Structures. Application to Lennard-Jones Atomic Clusters”, Pol. J. Chem. 1998, 72, 1849-1857.
7. Wawak, R.; Pillardy, J.; Liwo, A.; Gibson, K.D.; Scheraga, H.A.; “Diffusion Equation and Distance Scaling Methods of Global Optimization; Applications to Crystal Structure Prediction”, J. Phys. Chem. A, 1998, 102, 2904-2918.
8. Liwo, A.; Pillardy, J.; Kazmierkiewicz, R.; Wawak, R.J.; Groth, M.; Czaplewski, C.; Oldziej, S.; Scheraga, H.A.; “Prediction of protein structure using a knowledge-based off-lattice united-residue force field and global optimization methods”, Theoretical Chemistry Accounts, 1999, 101, 16-20.
9. Liwo, A.; Lee, J.; Ripoll, D.R.; Pillardy, J.; Scheraga, H.A.; “Protein structure prediction by global optimization of a potential energy function”, Proc. Natl. Acad. Sci., USA, 1999, 96, 5482-5485.
10. Lee, J.; Liwo, A.; Ripoll, D.R.; Pillardy J.; Scheraga, H.A.; “Calculation of protein conformation by global optimization of a potential energy function”, Proteins: Structure, Function and Genetics 1999, Suppl. 3, 204-208.
11. Scheraga, H.A.; Lee, J.; Pillardy, J.; Ye, Y.-J.; Liwo, A.; Ripoll, D.R.; “Surmounting the multiple-minima problem in protein folding”, J. Global Optimization 1999, 15, 235-260.
12. Pillardy, J.; Liwo, A.; Groth, M.; Scheraga, H.A.; “An efficient deformation-based global optimization method for off-lattice polymer chains; self-consistent basin-to-deformed-basin mapping (SCBDBM). Application to united-residue polypeptide chains”, J. Phys. Chem. B 1999, 103, 7353-7366.
13. Pillardy, J.; Liwo, A.; Scheraga, H.A.; “An efficient deformation-based global optimization method [self-consistent basin-to-deformed-basin mapping (SCBDBM)]; Application to Lennard-Jones atomic clusters”, J. Phys. Chem. A 1999, 103, 9370-9377.
14. Lee, J.; Liwo, A.; Ripoll, D.R.; Pillardy, J.; Saunders, J.; Gibson, K.D.; Scheraga, H.A.; “Hierarchical energy-based approach to protein-structure prediction -- blind-test evaluation on CASP targets”, Int. J. Quant. Chem. 2000, 71, 90-117.
15. Pillardy, J.; Wawak, R.; Arnautova, Y.; Czaplewski, C.; Scheraga, H.A.; “Crystal Structure Prediction by Global Optimization as a Tool for Evaluating Potentials; Role of the Dipole Moment Correction Term in Successful Predictions”, J. Am. Chem. Soc. 2000, 122, 907-921.
16. Lee, J.; Pillardy, J.; Czaplewski, C.; Arnautova, Y.; Ripoll, D.R.; Liwo, A.; Gibson, K.D.; Wawak, R; Scheraga, H.A.; “Efficient parallel algorithms in global optimization of potential energy functions”, Comp. Phys. Comm. 2000, 128, 399-411.
17. Wedemeyer, W. J.; Arnautova, Y. A.; Pillardy, J.; Wawak, R. J.; Czaplewski, C.; Scheraga, H. A.; “Reply to "Comment on 'Crystal Structure Prediction by Global Optimization as a Tool for Evaluating Potentials: Role of the Dipole Moment Correction Term in Successful Predictions'" by B. P. van Eijck and J. Kroon”, J. Phys. Chem. B 2000, 104, 8090-8092.
18. Pillardy, J; Czaplewski, C; Wedemeyer, W. J.; Scheraga, H. A.; “Conformation-Family Monte Carlo (CFMC): An efficient computational method for identifying the low-energy states of a macromolecule” Helvetica Chimica Acta, 2000, 83, 2214-2230.
19. Liwo, A.; Pillardy, J.; Czaplewski, C.; Lee, J.; Ripoll, D. R.; Groth, M.; Rodziewicz- Motowidlo, S.; Kazmierkiewicz, R.; Wawak, R. J.; Oldziej, S.; Scheraga, H. A.; “UNRES - a united-residue force field for energy-based prediction of protein structure - origin and significance of multibody terms”, RECOMB 2000, Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000, 193-200.
20. Pillardy J.; Czaplewski C.; Liwo A.; Lee J.; Ripoll D. R.; Kazmierkiewicz R.; Oldziej S.; Wedemeyer W. J.; Gibson K. D.; Arnautova Y. A.; Saunders J; Ye Y. J.; Scheraga H. A.; “Recent improvements in prediction of protein structure by global optimization of a potential energy function”, Proc. Natl. Acad. Sci., USA, 2001, 98, 2329-2333.
21. Liwo, A; Czaplewski, C.; Pillardy, J.; Scheraga, H. A.; “Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field” J. Chem. Phys. 2001, 115, 2323-2347.
22. Lee J.; Ripoll D. R.; Czaplewski C.; Pillardy J.; Wedemeyer W. J.; Scheraga H. A.; “Optimization of parameters in macromolecular potential energy functions by conformational space annealing” J. Phys. Chem. B 2001, 105, 7291-7298.
23. Pillardy J.; Czaplewski C.; Liwo A.; Wedemeyer W. J.; Lee J.; Ripoll D. R.; Arlukowicz P.; Oldziej S.; Arnautova Y. A.; Scheraga H. A.; “Development of physics-based energy functions that predict medium-resolution structures for proteins of the alpha,beta and alpha/beta structural classes” J. Phys. Chem. B 2001, 105, 7299-7311.
24. Pillardy J.; Arnautova Y. A.; Czaplewski C.; Gibson K. D.; Scheraga H. A.; “Conformation-Family Monte Carlo – A New Method for Crystal Structure Prediction”, Proc. Natl. Acad. Sci., USA, 2001, 98, 12351-12356.
25. Scheraga H. A.; Pillardy J.; Liwo A.; Lee J.; Czaplewski C.; Ripoll D. R.; Wedemeyer W. J.; Arnautova Y. A.; “Evolution of physics-based methodology for exploring the conformational energy landscape of proteins”, J. Comp. Chem., 2002, 23, 28-34.
26. Liwo A.; Arlukowicz P.; Czaplewski C.; Oldziej S.; Pillardy J.; Scheraga H. A.; “A novel method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape; application to the UNRES force field ”, Proc. Natl. Acad. Sci., USA, 2002, 99, 1937-1942.
27. Arnautova Y. A.; Pillardy J.; Czaplewski C.; Scheraga H. A.; “Global Optimization-Based Method for Deriving Intermolecular Potential Parameters for Crystals” J. Phys. Chem. B 2003, 107, 712-723.
28. Nanias, M.; Chinchio, M.; Pillardy, J.; Ripoll, D. R.; Scheraga H. A.; "Packing helices in proteins by global optimization of a potential energy function", Proc. Natl. Acad. Sci., USA, 2003, 100, 1706-1710.
29. Sidjanin, D. J.; Miller, B.; Kijas, J.; McElwee, J.; Pillardy, J.; Malek, J.; Pai, G.; Feldblyum, T.; Fraser, C.; Ackland, G.; Aguirre, G.; "Radiation hybrid map, physical map, and low-pass genomic sequence of the canine prcd region on CFA9 and comparative mapping with the syntenic region on human chromosome 17", Genomics, 2003, 81, 138-148.
30. Arnautova Y. A.; Jagielska A.; Pillardy J.; Scheraga H. A.; “Derivation of a new force field for crystal-structure prediction using global optimization: Nonbonded potential parameters for hydrocarbons and alcohols” J. Phys. Chem. B 2003, 107, 7143-7154.
31. Czaplewski, C.; Liwo, A.; Pillardy, J; Ołdziej, S; Scheraga, H. A.; “Improved Conformational Space Annealing method to treat b-structure with the UNRES force-field and to enhance scalability of parallel implementation” Polymer, 2004, 45, 677-686.
32. Teodorescu, O.; Galor, T.; Pillardy, J; Elber, R; “Enriching the sequence substitution matrix by structural information”, Proteins, Structure, Function and Genetics, 2004, 54, 41-48.
33. Peltier, J. B.; Ripoll, D. R.; Friso, G.; Rudella, A.; Cai, Y.; Ytterberg, J.; Giacomelli, L.; Pillardy J.; van Wijk, K. J. “Clp Protease Complexes from Photosynthetic and Non-photosynthetic Plastids and Mitochondria of Plants, Their Predicted Three-dimensional Structures, and Functional Implications” J. Biol. Chem., 2004, 279, 4768-4781.
34. Scheraga, H.A.; Liwo, A.; Oldziej, S.; Czaplewski, C.; Pillardy, J.; Ripoll, D.R.; Vila, J.A.; Kazmierkiewicz, R.; Arnautova, Y.A.; Jagielska, A.; Chinchio, M.; and Nanias, M.; “The Protein Folding Problem: Force Field and Global Optimization.” Frontiers in Bioscience, 2004, 9, 3296-3323.
35. Odziej, S.; Liwo, A.; Czaplewski, C.; Pillardy, J.; Scheraga, H. A."Optimization
of the UNRES Force Field by Hierarchical Design of the Potential-Energy
Landscape. 2. Off-Lattice Tests of the Method with Single Proteins."
J. Phys. Chem. B,
36. Oldziej, S.; Czaplewski, C.; Liwo, A.; Chinchio, M.; Nanias, M.; Vila, J.A.; Khalili, M.; Arnautova, Y.A.; Jagielska, A.; Makowski, M.; Schafroth, H.D.; Kazmierkiewicz, R.; Ripoll D.R.; Pillardy, J.; Saunders, J.A.; Kang Y.K.; Gibson K.D.; Scheraga, H.A. "Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: Assessment in two blind tests" Proc. Natl. Acad. Sci., USA, 2005, 102, 7547-7552.
37. Zangerl, B.; Sun, Q.; Pillardy, J.; Johnson, JL.; Schweitzer, PA.; Hernandez, AG.; Liu, L.; Acland, GM.; Aguirre, GD.; "Development and characterization of a normalized canine retinal cDNA library for genomic and expression studies" Investigative Ophthalmology & Visual Science, 2006, 47 (6), 2632-2638.
38. Yu, Chun-Nam J.; Joachims, T.; Elber, R.; Pillardy, J.; "Support vector training of protein alignment models" Research in Computational Molecular Biology, Proceedings 2007, 253-267 (in LECTURE NOTES IN COMPUTER SCIENCE 4453).
39. Vallat, BK; Pillardy, J; Elber, R; “A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins“ Proteins - Structure Function and Bioinformatics 2008, 72 (3), 910-928.
40.Yu, CNJ; Joachims, T; Elber, R; Pillardy, J; “Support vector training of protein alignment models” J. Comp. Biol. 2008, 15 (7), 867-880.
41. Zangerl, B; Johnson, J L; Pillardy, J; Sun, Q; Andre, C; Galibert, F; Acland, G M; Aguirre, G D; "Comparative genomic mapping of uncharacterized canine retinal ESTs to identify novel candidate genes for hereditary retinal disorders ", Molecular Vision, 2009, 15 (97), 927-936.
42. Vallat, B K; Pillardy J; Majek P; Meller J; Blom T; Cao BQ; Elber R; "Building and assessing atomic models of proteins from structural templates: Learning and benchmarks", Proteins: Structure, Function and Bioinformatics, 2009, 76 (4), 930-945.