Harold A. Scheraga

45 papers A 1B 1C 1Misc 1Journal 38Unranked 2

Year	Rank	Type	Title / Venue / Authors
2018	J	`jnl`	A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields. J. Comput. Chem. Adam K. Sieradzan, Artur Gieldon, Yanping Yin, Yi He, Harold A. Scheraga, Adam Liwo
2018	J	`jnl`	Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. J. Chem. Inf. Model. Pawel Krupa, Anna Halabis, Wioletta Zmudzinska, Stanislaw Oldziej, Harold A. Scheraga, Adam Liwo
2017	J	`jnl`	Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. J. Chem. Inf. Model. Pawel Krupa, Anna Halabis, Wioletta Zmudzinska, Stanislaw Oldziej, Harold A. Scheraga, Adam Liwo
2016	J	`jnl`	Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. Bioinform. Pawel Krupa, Magdalena A. Mozolewska, Marta Wisniewska, Yanping Yin, Yi He, Adam K. Sieradzan, Robert Ganzynkowicz, Agnieszka G. Lipska, Agnieszka S. Karczynska, Magdalena Slusarz, Rafal Slusarz, Artur Gieldon, Cezary Czaplewski, Dawid Jagiela, Bartlomiej Zaborowski, Harold A. Scheraga, Adam Liwo
2014	J	`jnl`	Are accurate computations of the J. Comput. Chem. Jorge A. Vila, Yelena A. Arnautova, Osvaldo A. Martin, Harold A. Scheraga
2014	J	`jnl`	Factors affecting the computation of the J. Comput. Chem. Pablo G. Garay, Osvaldo A. Martin, Harold A. Scheraga, Jorge A. Vila
2010	J	`jnl`	Coarse-grained model of nucleic acid bases. J. Comput. Chem. Maciej Maciejczyk, Aleksandar Spasic, Adam Liwo, Harold A. Scheraga
2010	J	`jnl`	Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. I. The method. J. Comput. Chem. Urszula Kozlowska, Adam Liwo, Harold A. Scheraga
2010	J	`jnl`	Determination of side-chain-rotamer and side-chain and backbone virtual-bond-stretching potentials of mean force from AM1 energy surfaces of terminally-blocked amino-acid residues, for coarse-grained simulations of protein structure and folding. II. Results, comparison with statistical potentials, and implementation in the UNRES force field. J. Comput. Chem. Urszula Kozlowska, Gia G. Maisuradze, Adam Liwo, Harold A. Scheraga
2010	C	`conf`	Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations. BIBE Stanislaw Oldziej, Cezary Czaplewski, Adam Liwo, Harold A. Scheraga
2009	J	`jnl`	Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field. J. Comput. Chem. Yi He, Yi Xiao, Adam Liwo, Harold A. Scheraga
2009	—	`ch.`	Global Optimization in Protein Folding. Encyclopedia of Optimization Daniel R. Ripoll, Adam Liwo, Harold A. Scheraga
2009	J	`jnl`	Performance of density functional models to reproduce observed J. Comput. Chem. Jorge A. Vila, Héctor A. Baldoni, Harold A. Scheraga
2007	J	`jnl`	Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: All-atom molecular dynamics in implicit solvent. J. Comput. Chem. Anna Jagielska, Harold A. Scheraga
2006	J	`jnl`	A Hierarchical Multiscale Approach to Protein Structure Prediction: Production of Low-Resolution Packing Arrangements of Helices and Refinement of the Best Models with a United-Residue Force Field. Multiscale Model. Simul. Maurizio Chinchio, Cezary Czaplewski, Stanislaw Oldziej, Harold A. Scheraga
2005	J	`jnl`	Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC. J. Comput. Chem. Marian Nanias, Maurizio Chinchio, Stanislaw Oldziej, Cezary Czaplewski, Harold A. Scheraga
2002	Misc	`conf`	Ab Initio Folding of Multiple-Chain Proteins. Pacific Symposium on Biocomputing J. A. Saunders, Kenneth D. Gibson, Harold A. Scheraga
2002	J	`jnl`	Energy-based reconstruction of a protein backbone from its -carbon trace by a Monte-Carlo method. J. Comput. Chem. Rajmund Kazmierkiewicz, Adam Liwo, Harold A. Scheraga
2002	J	`jnl`	Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. J. Comput. Chem. Harold A. Scheraga, Jaroslaw Pillardy, Adam Liwo, Jooyoung Lee, Cezary Czaplewski, Daniel R. Ripoll, William J. Wedemeyer, Yelena A. Arnautova
2000	B	`conf`	UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody terms. RECOMB Adam Liwo, Jaroslaw Pillardy, Cezary Czaplewski, Jooyoung Lee, Daniel R. Ripoll, Malgorzata Groth, Sylwia Rodziewicz-Motowidlo, Rajmund Kazmierkiewicz, Ryszard J. Wawak, Stanislaw Oldziej, Harold A. Scheraga
1999	J	`jnl`	Exact analytical loop closure in proteins using polynomial equations. J. Comput. Chem. William J. Wedemeyer, Harold A. Scheraga
1999	J	`jnl`	Flexible docking simulations: Scaled collective variable Monte Carlo minimization approach using Bezier splines, and comparison with a standard Monte Carlo algorithm. J. Comput. Chem. Jean-Yves Trosset, Harold A. Scheraga
1999	J	`jnl`	Prodock: Software package for protein modeling and docking. J. Comput. Chem. Jean-Yves Trosset, Harold A. Scheraga
1999	J	`jnl`	Surmounting the Multiple-Minima Problem in Protein Folding. J. Glob. Optim. Harold A. Scheraga, Jooyoung Lee, Jaroslaw Pillardy, Yuan-Jie Ye, Adam Liwo, Daniel R. Ripoll
1998	J	`jnl`	B-spline method for energy minimization in grid-based molecular mechanics calculations. J. Comput. Chem. Daniel Oberlin, Harold A. Scheraga
1998	J	`jnl`	United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials. J. Comput. Chem. Adam Liwo, Rajmund Kazmierkiewicz, Cezary Czaplewski, Malgorzata Groth, Stanislaw Oldziej, Ryszard J. Wawak, Shelly Rackovsky, Matthew R. Pincus, Harold A. Scheraga
1997	J	`jnl`	A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent. J. Comput. Chem. Yury N. Vorobjev, Harold A. Scheraga
1997	J	`jnl`	A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data. J. Comput. Chem. Adam Liwo, Stanislaw Oldziej, Matthew R. Pincus, Ryszard J. Wawak, Shelly Rackovsky, Harold A. Scheraga
1997	J	`jnl`	A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization. J. Comput. Chem. Adam Liwo, Matthew R. Pincus, Ryszard J. Wawak, Shelly Rackovsky, Stanislaw Oldziej, Harold A. Scheraga
1997	J	`jnl`	An assessment of the accuracy of the RRIGS hydration potential: Comparison to solutions of the Poisson-Boltzmann equation. J. Comput. Chem. Joseph D. Augspurger, Harold A. Scheraga
1997	J	`jnl`	Energy minimization of rigid-geometry polypeptides with exactly closed disulfide loops. J. Comput. Chem. Kenneth D. Gibson, Harold A. Scheraga
1997	J	`jnl`	New optimization method for conformational energy calculations on polypeptides: Conformational space annealing. J. Comput. Chem. Jooyoung Lee, Harold A. Scheraga, Shelly Rackovsky
1996	J	`jnl`	An efficient, differentiable hydration potential for peptides and proteins. J. Comput. Chem. Joseph D. Augspurger, Harold A. Scheraga
1996	J	`jnl`	From secondary structure to three-dimensional structure: Improved dihedral angle probability distribution function for use with energy searches for native structures of polypeptides and proteins. J. Comput. Chem. Betty Cheng, Akbar Nayeem, Harold A. Scheraga
1996	—	`conf`	Implementation of ECEPP-Based Programs on the IBM SP2 and the SGI Power Challenge Computers. HPCN Europe Timothy J. O'Donnell, Steven Hotovy, Marcia S. Pottle, Daniel R. Ripoll, Harold A. Scheraga
1995	A	`conf`	Computational Approach to the Statistical Mechanics of Protein Folding. SC Ming-Hong Hao, Harold A. Scheraga
1995	J	`jnl`	Determination of Net Atomics Charges Using a Modified Partial Equalization or Orbital Electronegativity Method. IC. Application to Hypervalent Sulfur and Phosphorus-Containing Molecules. J. Comput. Chem. Je Myung Park, Oh Young Kwon, Kyoung Tai No, Mu Shik Jhon, Harold A. Scheraga
1995	J	`jnl`	Implementation of the ECEPP Algorithm, the Monte Carlo Minimization Method, and the Electrostatically Driven Monte Carlo Method on the Kendall Square Research KSR1 Computer. J. Comput. Chem. Daniel R. Ripoll, Marcia S. Pottle, Kenneth D. Gibson, Harold A. Scheraga, Adam Liwo
1995	J	`jnl`	Simple global minimization algorithm for one-variable rational functions. J. Glob. Optim. Jaroslaw Kostrowicki, Harold A. Scheraga
1995	—	`conf`	Some approaches to the multiple-minima problem in protein folding. Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding Jaroslaw Kostrowicki, Harold A. Scheraga
1994	J	`jnl`	A Rapid and Efficient Algorithm for Packing Polypeptide Chains by Energy Minimization. J. Comput. Chem. Kenneth D. Gibson, Harold A. Scheraga
1994	J	`jnl`	An Algorithm for Packing Regular Multistrand Polypeptide Structures by Energy Minimization. J. Comput. Chem. Kenneth D. Gibson, Harold A. Scheraga
1993	J	`jnl`	Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. III. Application to halogenated and aromatic molecules. J. Comput. Chem. Je Myung Park, Kyoung Tai No, Mu Shik Jhon, Harold A. Scheraga
1991	J	`jnl`	U-3'-BCIP: a chromogenic substrate for the detection of RNase A in recombinant DNA expression systems. Nucleic Acids Res. M. R. Witmer, C. M. Falcomer, M. P. Weiner, M. S. Kay, T. P. Begley, B. Ganem, Harold A. Scheraga
1989	J	`jnl`	A set of Macintosh computer programs for the design and analysis of synthetic genes. Comput. Appl. Biosci. M. P. Weiner, Harold A. Scheraga