Harold A. Scheraga

Osvaldo A. Martin, Jorge A. Vila, Harold A. Scheraga: CheShift-2: graphic validation of protein structures. Bioinformatics 28(11): 1538-1539 (2012)

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. Journal of Computational Chemistry 31(6): 1143-1153 (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. Journal of Computational Chemistry 31(6): 1154-1167 (2010)

Maciej Maciejczyk, Aleksandar Spasic, Adam Liwo, Harold A. Scheraga: Coarse-grained model of nucleic acid bases. Journal of Computational Chemistry 31(8): 1644-1655 (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: 263-266

Jorge A. Vila, Héctor A. Baldoni, Harold A. Scheraga: Performance of density functional models to reproduce observed ¹³C^alpha chemical shifts of proteins in solution. Journal of Computational Chemistry 30(6): 884-892 (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. Journal of Computational Chemistry 30(13): 2127-2135 (2009)

Daniel R. Ripoll, Adam Liwo, Harold A. Scheraga: Global Optimization in Protein Folding. Encyclopedia of Optimization 2009: 1392-1411

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. Journal of Computational Chemistry 28(6): 1068-1082 (2007)

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. Journal of Computational Chemistry 26(14): 1472-1486 (2005)

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. Journal of Computational Chemistry 23(1): 28-34 (2002)

Rajmund Kazmierkiewicz, Adam Liwo, Harold A. Scheraga: Energy-based reconstruction of a protein backbone from its -carbon trace by a Monte-Carlo method. Journal of Computational Chemistry 23(7): 715-723 (2002)

J. A. Saunders, Kenneth D. Gibson, Harold A. Scheraga: Ab Initio Folding of Multiple-Chain Proteins. Pacific Symposium on Biocomputing 2002: 601-612

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: 193-200

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. Journal of Computational Chemistry 20(2): 244-252 (1999)

Jean-Yves Trosset, Harold A. Scheraga: Prodock: Software package for protein modeling and docking. Journal of Computational Chemistry 20(4): 412-427 (1999)

William J. Wedemeyer, Harold A. Scheraga: Exact analytical loop closure in proteins using polynomial equations. Journal of Computational Chemistry 20(8): 819-844 (1999)

Daniel Oberlin, Harold A. Scheraga: B-spline method for energy minimization in grid-based molecular mechanics calculations. Journal of Computational Chemistry 19(1): 71-85 (1998)

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. Journal of Computational Chemistry 19(3): 259-276 (1998)

Kenneth D. Gibson, Harold A. Scheraga: Energy minimization of rigid-geometry polypeptides with exactly closed disulfide loops. Journal of Computational Chemistry 18(3): 403-415 (1997)

Yury N. Vorobjev, Harold A. Scheraga: A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent. Journal of Computational Chemistry 18(4): 569-583 (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. Journal of Computational Chemistry 18(7): 849-873 (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. Journal of Computational Chemistry 18(7): 874-887 (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. Journal of Computational Chemistry 18(8): 1072-1078 (1997)

Jooyoung Lee, Harold A. Scheraga, Shelly Rackovsky: New optimization method for conformational energy calculations on polypeptides: Conformational space annealing. Journal of Computational Chemistry 18(9): 1222-1232 (1997)

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. Journal of Computational Chemistry 17(12): 1453-1480 (1996)

Joseph D. Augspurger, Harold A. Scheraga: An efficient, differentiable hydration potential for peptides and proteins. Journal of Computational Chemistry 17(13): 1549-1558 (1996)

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: 365-372

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. Journal of Computational Chemistry 16(8): 1011-1027 (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. Journal of Computational Chemistry 16(9): 1153-1163 (1995)

Ming-Hong Hao, Harold A. Scheraga: Computational Approach to the Statistical Mechanics of Protein Folding. SC 1995: 21

Kenneth D. Gibson, Harold A. Scheraga: A Rapid and Efficient Algorithm for Packing Polypeptide Chains by Energy Minimization. Journal of Computational Chemistry 15(12): 1403-1413 (1994)

Kenneth D. Gibson, Harold A. Scheraga: An Algorithm for Packing Regular Multistrand Polypeptide Structures by Energy Minimization. Journal of Computational Chemistry 15(12): 1414-1428 (1994)

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 Research 19(1): 1-4 (1991)

M. P. Weiner, Harold A. Scheraga: A set of Macintosh computer programs for the design and analysis of synthetic genes. Computer Applications in the Biosciences 5(3): 191-198 (1989)