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Harold A. Scheraga

Publication Activity (10 Years)

Years Active: 1989-2018
Publications (10 Years): 4

Top Topics

Protein Structure

Amino Acid Sequences

Maximum Likelihood

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

Publications

Adam K. Sieradzan, Artur Gieldon, Yanping Yin, Yi He, Harold A. Scheraga, Adam Liwo
A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields. J. Comput. Chem. 39 (28) (2018)
Pawel Krupa, Anna Halabis, Wioletta Zmudzinska, Stanislaw Oldziej, Harold A. Scheraga, Adam Liwo
Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. J. Chem. Inf. Model. 58 (1) (2018)
Pawel Krupa, Anna Halabis, Wioletta Zmudzinska, Stanislaw Oldziej, Harold A. Scheraga, Adam Liwo
Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. J. Chem. Inf. Model. 57 (9) (2017)
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
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. Bioinform. 32 (21) (2016)
Pablo G. Garay, Osvaldo A. Martin, Harold A. Scheraga, Jorge A. Vila
C shielding in disaccharides. J. Comput. Chem. 35 (25) (2014)
Jorge A. Vila, Yelena A. Arnautova, Osvaldo A. Martin, Harold A. Scheraga
C′ shielding feasible at the DFT level of theory? J. Comput. Chem. 35 (4) (2014)
Osvaldo A. Martin, Jorge A. Vila, Harold A. Scheraga
Shift-2: graphic validation of protein structures. Bioinform. 28 (11) (2012)
Maciej Maciejczyk, Aleksandar Spasic, Adam Liwo, Harold A. Scheraga
Coarse-grained model of nucleic acid bases. J. Comput. Chem. 31 (8) (2010)
Urszula Kozlowska, Adam Liwo, Harold A. Scheraga
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. 31 (6) (2010)
Stanislaw Oldziej, Cezary Czaplewski, Adam Liwo, Harold A. Scheraga
Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations. BIBE (2010)
Urszula Kozlowska, Gia G. Maisuradze, Adam Liwo, Harold A. Scheraga
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. 31 (6) (2010)
Jorge A. Vila, Héctor A. Baldoni, Harold A. Scheraga
chemical shifts of proteins in solution. J. Comput. Chem. 30 (6) (2009)
Yi He, Yi Xiao, Adam Liwo, Harold A. Scheraga
Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field. J. Comput. Chem. 30 (13) (2009)
Anna Jagielska, Harold A. Scheraga
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. 28 (6) (2007)
Maurizio Chinchio, Cezary Czaplewski, Stanislaw Oldziej, Harold A. Scheraga
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. 5 (4) (2006)
Marian Nanias, Maurizio Chinchio, Stanislaw Oldziej, Cezary Czaplewski, Harold A. Scheraga
Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC. J. Comput. Chem. 26 (14) (2005)
J. A. Saunders, Kenneth D. Gibson, Harold A. Scheraga
Ab Initio Folding of Multiple-Chain Proteins. Pacific Symposium on Biocomputing (2002)
Harold A. Scheraga, Jaroslaw Pillardy, Adam Liwo, Jooyoung Lee, Cezary Czaplewski, Daniel R. Ripoll, William J. Wedemeyer, Yelena A. Arnautova
Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. J. Comput. Chem. 23 (1) (2002)
Rajmund Kazmierkiewicz, Adam Liwo, Harold A. Scheraga
Energy-based reconstruction of a protein backbone from its -carbon trace by a Monte-Carlo method. J. Comput. Chem. 23 (7) (2002)
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
UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody terms. RECOMB (2000)
Jean-Yves Trosset, Harold A. Scheraga
Prodock: Software package for protein modeling and docking. J. Comput. Chem. 20 (4) (1999)
Harold A. Scheraga, Jooyoung Lee, Jaroslaw Pillardy, Yuan-Jie Ye, Adam Liwo, Daniel R. Ripoll
Surmounting the Multiple-Minima Problem in Protein Folding. J. Glob. Optim. 15 (3) (1999)
William J. Wedemeyer, Harold A. Scheraga
Exact analytical loop closure in proteins using polynomial equations. J. Comput. Chem. 20 (8) (1999)
Jean-Yves Trosset, Harold A. Scheraga
Flexible docking simulations: Scaled collective variable Monte Carlo minimization approach using Bezier splines, and comparison with a standard Monte Carlo algorithm. J. Comput. Chem. 20 (2) (1999)
Adam Liwo, Rajmund Kazmierkiewicz, Cezary Czaplewski, Malgorzata Groth, Stanislaw Oldziej, Ryszard J. Wawak, Shelly Rackovsky, Matthew R. Pincus, Harold A. Scheraga
United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials. J. Comput. Chem. 19 (3) (1998)
Daniel Oberlin, Harold A. Scheraga
B-spline method for energy minimization in grid-based molecular mechanics calculations. J. Comput. Chem. 19 (1) (1998)
Yury N. Vorobjev, Harold A. Scheraga
A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent. J. Comput. Chem. 18 (4) (1997)
Joseph D. Augspurger, Harold A. Scheraga
An assessment of the accuracy of the RRIGS hydration potential: Comparison to solutions of the Poisson-Boltzmann equation. J. Comput. Chem. 18 (8) (1997)
Jooyoung Lee, Harold A. Scheraga, Shelly Rackovsky
New optimization method for conformational energy calculations on polypeptides: Conformational space annealing. J. Comput. Chem. 18 (9) (1997)
Kenneth D. Gibson, Harold A. Scheraga
Energy minimization of rigid-geometry polypeptides with exactly closed disulfide loops. J. Comput. Chem. 18 (3) (1997)
Adam Liwo, Matthew R. Pincus, Ryszard J. Wawak, Shelly Rackovsky, Stanislaw Oldziej, Harold A. Scheraga
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. 18 (7) (1997)
Adam Liwo, Stanislaw Oldziej, Matthew R. Pincus, Ryszard J. Wawak, Shelly Rackovsky, Harold A. Scheraga
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. 18 (7) (1997)
Timothy J. O'Donnell, Steven Hotovy, Marcia S. Pottle, Daniel R. Ripoll, Harold A. Scheraga
Implementation of ECEPP-Based Programs on the IBM SP2 and the SGI Power Challenge Computers. HPCN Europe (1996)
Joseph D. Augspurger, Harold A. Scheraga
An efficient, differentiable hydration potential for peptides and proteins. J. Comput. Chem. 17 (13) (1996)
Betty Cheng, Akbar Nayeem, Harold A. Scheraga
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. 17 (12) (1996)
Jaroslaw Kostrowicki, Harold A. Scheraga
Simple global minimization algorithm for one-variable rational functions. J. Glob. Optim. 6 (3) (1995)
Daniel R. Ripoll, Marcia S. Pottle, Kenneth D. Gibson, Harold A. Scheraga, Adam Liwo
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. 16 (9) (1995)
Je Myung Park, Oh Young Kwon, Kyoung Tai No, Mu Shik Jhon, Harold A. Scheraga
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. 16 (8) (1995)
Ming-Hong Hao, Harold A. Scheraga
Computational Approach to the Statistical Mechanics of Protein Folding. SC (1995)
Jaroslaw Kostrowicki, Harold A. Scheraga
Some approaches to the multiple-minima problem in protein folding. Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding (1995)
Kenneth D. Gibson, Harold A. Scheraga
A Rapid and Efficient Algorithm for Packing Polypeptide Chains by Energy Minimization. J. Comput. Chem. 15 (12) (1994)
Kenneth D. Gibson, Harold A. Scheraga
An Algorithm for Packing Regular Multistrand Polypeptide Structures by Energy Minimization. J. Comput. Chem. 15 (12) (1994)
Je Myung Park, Kyoung Tai No, Mu Shik Jhon, Harold A. Scheraga
Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. III. Application to halogenated and aromatic molecules. J. Comput. Chem. 14 (12) (1993)
M. R. Witmer, C. M. Falcomer, M. P. Weiner, M. S. Kay, T. P. Begley, B. Ganem, Harold A. Scheraga
U-3'-BCIP: a chromogenic substrate for the detection of RNase A in recombinant DNA expression systems. Nucleic Acids Res. 19 (1) (1991)
M. P. Weiner, Harold A. Scheraga
A set of Macintosh computer programs for the design and analysis of synthetic genes. Comput. Appl. Biosci. 5 (3) (1989)