Physics-Based Protein-Structure Prediction Using a Hierarchical Protocol Based on the UNRES Force Field: Assessment in Two Blind Tests von Ołdziej, S., Czaplewski, C., Liwo, A., Chinchio, M., Nanias, M., Vila, J. A., Khalili, M., Arnautova, Y. A., Jagielska, A., Makowski, M., Schafroth, H. D., Kaźmierkiewicz, R., Ripoll, D. R., Pillardy, J., Saunders, J. A., Kang, Y. K., Gibson, K. D., Scheraga, H. A.

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Cumulant-based expressions for the multibody terms for the correlation between local and electrostatic interactions in the united-residue force field von Liwo, Adam, Czaplewski, Cezary, Pillardy, Jarosław, Scheraga, Harold A.

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Comparative genomic mapping of uncharacterized canine retinal ESTs to identify novel candidate genes for hereditary retinal disorders von Zangerl, B, Johnson, J L, Pillardy, J, Sun, Q, André, C, Galibert, F, Acland, G M, Aguirre, G D

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Clp Protease Complexes from Photosynthetic and Non-photosynthetic Plastids and Mitochondria of Plants, Their Predicted Three-dimensional Structures, and Functional Implications von Peltier, Jean-Benoît, Ripoll, Daniel R., Friso, Giulia, Rudella, Andrea, Cai, Yang, Ytterberg, Jimmy, Giacomelli, Lisa, Pillardy, Jaroslaw, van Wijk, Klaas J.

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Enriching the sequence substitution matrix by structural information von Teodorescu, Octavian, Galor, Tamara, Pillardy, Jaroslaw, Elber, Ron

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Recent Improvements in Prediction of Protein Structure by Global Optimization of a Potential Energy Function von Pillardy, Jarosław, Czaplewski, Cezary, Liwo, Adam, Lee, Jooyoung, Ripoll, Daniel R., Kaźmierkiewicz, Rajmund, Ołdziej, Stanisław, Wedemeyer, William J., Gibson, Kenneth D., Arnautova, Yelena A., Saunders, Jeff, Ye, Yuan-Jie, Scheraga, Harold A.

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A Method for Optimizing Potential-Energy Functions by a Hierarchical Design of the Potential-Energy Landscape: Application to the UNRES Force Field von Liwo, Adam, Arłukowicz, Piotr, Czaplewski, Cezary, Ołdziej, Stanisław, Pillardy, Jarosław, Scheraga, Harold A.

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P43-S Computational Biology Applications Suite for High-Performance Computing (BioHPC.net) von Pillardy, J.

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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 von Sidjanin, D.J, Miller, B, Kijas, J, McElwee, J, Pillardy, J, Malek, J, Pai, G, Feldblyum, T, Fraser, C, Acland, G, Aguirre, G

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Optimization of the UNRES Force Field by Hierarchical Design of the Potential-Energy Landscape. 2. Off-Lattice Tests of the Method with Single Proteins von Ołdziej, Stanisław, Liwo, Adam, Czaplewski, Cezary, Pillardy, Jarosław, Scheraga, Harold A

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Protein Structure Prediction by Global Optimization of a Potential Energy Function von Liwo, Adam, Lee, Jooyoung, Ripoll, Daniel R., Pillardy, Jaroslaw, Scheraga, Harold A.

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Support vector training of protein alignment models von Yu, Chun-Nam John, Joachims, Thorsten, Elber, Ron, Pillardy, Jaroslaw

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Packing Helices in Proteins by Global Optimization of a Potential Energy Function von Nanias, Marian, Chinchio, Maurizio, Pillardy, Jarosław, Ripoll, Daniel R., Scheraga, Harold A.

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Optimization of Parameters in Macromolecular Potential Energy Functions by Conformational Space Annealing von Lee, Jooyoung, Ripoll, Daniel R, Czaplewski, Cezary, Pillardy, Jarosław, Wedemeyer, William J, Scheraga, Harold A

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BioHPC: Computational Biology Application Suite for High Performance Computing von Bukowski, R., Sun, Q., Howard, M., Pillardy, J.

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Improved conformational space annealing method to treat β-structure with the UNRES force-field and to enhance scalability of parallel implementation von Czaplewski, Cezary, Liwo, Adam, Pillardy, Jarosław, Ołdziej, Stanisław, Scheraga, Harold A.

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Conformation-Family Monte Carlo: A New Method for Crystal Structure Prediction von Pillardy, Jaroslaw, Arnautova, Yelena A., Czaplewski, Cezary, Gibson, Kenneth D., Scheraga, Harold A.

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An Efficient Deformation-Based Global Optimization Method (Self-Consistent Basin-to-Deformed-Basin Mapping (SCBDBM)). Application to Lennard-Jones Atomic Clusters von Pillardy, Jarosław, Liwo, Adam, Scheraga, Harold A

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Development of Physics-Based Energy Functions that Predict Medium-Resolution Structures for Proteins of the α, β, and α/β Structural Classes von Pillardy, Jarosław, Czaplewski, Cezary, Liwo, Adam, Wedemeyer, William J, Lee, Jooyoung, Ripoll, Daniel R, Arłukowicz, Piotr, Ołdziej, Stanisław, Arnautova, Yelena A, Scheraga, Harold A

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Calculation of protein conformation by global optimization of a potential energy function von Lee, Jooyoung, Liwo, Adam, Ripoll, Daniel R., Pillardy, Jaroslaw, Scheraga, Harold A.

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