A set of Macintosh computer programs for the design and analysis of synthetic genes. - M. P. Weiner; Harold A. Scheraga (Comput. Appl. Biosci., 1989)

U-3'-BCIP: a chromogenic substrate for the detection of RNase A in recombinant DNA expression systems. - M. R. Witmer; C. M. Falcomer; M. P. Weiner; M. S. Kay; T. P. Begley; B. Ganem; Harold A. Scheraga (Nucleic Acids Res., 1991)

Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. III. Application to halogenated and aromatic molecules. - Je Myung Park; Kyoung Tai No; Mu Shik Jhon; Harold A. Scheraga (J. Comput. Chem., 1993)

A Rapid and Efficient Algorithm for Packing Polypeptide Chains by Energy Minimization. - Kenneth D. Gibson; Harold A. Scheraga (J. Comput. Chem., 1994)

An Algorithm for Packing Regular Multistrand Polypeptide Structures by Energy Minimization. - Kenneth D. Gibson; Harold A. Scheraga (J. Comput. Chem., 1994)

Some approaches to the multiple-minima problem in protein folding. - Jaroslaw Kostrowicki; Harold A. Scheraga (Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, 1995)

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

Determination of Net Atomics Charges Using a Modified Partial Equalization or Orbital Electronegativity Method. IC. Application to Hypervalent Sulfur and Phosphorus-Containing Molecules. - Je Myung Park; Oh Young Kwon; Kyoung Tai No; Mu Shik Jhon; Harold A. Scheraga (J. Comput. Chem., 1995)

Implementation of the ECEPP Algorithm, the Monte Carlo Minimization Method, and the Electrostatically Driven Monte Carlo Method on the Kendall Square Research KSR1 Computer. - Daniel R. Ripoll; Marcia S. Pottle; Kenneth D. Gibson; Harold A. Scheraga; Adam Liwo (J. Comput. Chem., 1995)

Simple global minimization algorithm for one-variable rational functions. - Jaroslaw Kostrowicki; Harold A. Scheraga (J. Glob. Optim., 1995)

Implementation of ECEPP-Based Programs on the IBM SP2 and the SGI Power Challenge Computers. - Timothy J. O'Donnell; Steven Hotovy; Marcia S. Pottle; Daniel R. Ripoll; Harold A. Scheraga (HPCN Europe, 1996)

An efficient, differentiable hydration potential for peptides and proteins. - Joseph D. Augspurger; Harold A. Scheraga (J. Comput. Chem., 1996)

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. - Betty Cheng; Akbar Nayeem; Harold A. Scheraga (J. Comput. Chem., 1996)

An assessment of the accuracy of the RRIGS hydration potential: Comparison to solutions of the Poisson-Boltzmann equation. - Joseph D. Augspurger; Harold A. Scheraga (J. Comput. Chem., 1997)

Energy minimization of rigid-geometry polypeptides with exactly closed disulfide loops. - Kenneth D. Gibson; Harold A. Scheraga (J. Comput. Chem., 1997)

New optimization method for conformational energy calculations on polypeptides: Conformational space annealing. - Jooyoung Lee 002; Harold A. Scheraga; Shelly Rackovsky (J. Comput. Chem., 1997)

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. - Adam Liwo; Stanislaw Oldziej; Matthew R. Pincus; Ryszard J. Wawak; Shelly Rackovsky; Harold A. Scheraga (J. Comput. Chem., 1997)

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. - Adam Liwo; Matthew R. Pincus; Ryszard J. Wawak; Shelly Rackovsky; Stanislaw Oldziej; Harold A. Scheraga (J. Comput. Chem., 1997)

A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent. - Yury N. Vorobjev; Harold A. Scheraga (J. Comput. Chem., 1997)

United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials. - Adam Liwo; Rajmund Kazmierkiewicz; Cezary Czaplewski; Malgorzata Groth; Stanislaw Oldziej; Ryszard J. Wawak; Shelly Rackovsky; Matthew R. Pincus; Harold A. Scheraga (J. Comput. Chem., 1998)

B-spline method for energy minimization in grid-based molecular mechanics calculations. - Daniel Oberlin; Harold A. Scheraga (J. Comput. Chem., 1998)

Flexible docking simulations: Scaled collective variable Monte Carlo minimization approach using Bezier splines, and comparison with a standard Monte Carlo algorithm. - Jean-Yves Trosset; Harold A. Scheraga (J. Comput. Chem., 1999)

Prodock: Software package for protein modeling and docking. - Jean-Yves Trosset; Harold A. Scheraga (J. Comput. Chem., 1999)

Exact analytical loop closure in proteins using polynomial equations. - William J. Wedemeyer; Harold A. Scheraga (J. Comput. Chem., 1999)

Surmounting the Multiple-Minima Problem in Protein Folding. - Harold A. Scheraga; Jooyoung Lee 002; Jaroslaw Pillardy; Yuan-Jie Ye; Adam Liwo; Daniel R. Ripoll (J. Glob. Optim., 1999)

UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody terms. - Adam Liwo; Jaroslaw Pillardy; Cezary Czaplewski; Jooyoung Lee 002; Daniel R. Ripoll; Malgorzata Groth; Sylwia Rodziewicz-Motowidlo; Rajmund Kazmierkiewicz; Ryszard J. Wawak; Stanislaw Oldziej; Harold A. Scheraga (RECOMB, 2000)

Ab Initio Folding of Multiple-Chain Proteins. - J. A. Saunders; Kenneth D. Gibson; Harold A. Scheraga (Pacific Symposium on Biocomputing, 2002)

Energy-based reconstruction of a protein backbone from its -carbon trace by a Monte-Carlo method. - Rajmund Kazmierkiewicz; Adam Liwo; Harold A. Scheraga (J. Comput. Chem., 2002)

Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. - Harold A. Scheraga; Jaroslaw Pillardy; Adam Liwo; Jooyoung Lee 002; Cezary Czaplewski; Daniel R. Ripoll; William J. Wedemeyer; Yelena A. Arnautova (J. Comput. Chem., 2002)

Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC. - Marian Nanias; Maurizio Chinchio; Stanislaw Oldziej; Cezary Czaplewski; Harold A. Scheraga (J. Comput. Chem., 2005)

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. - Maurizio Chinchio; Cezary Czaplewski; Stanislaw Oldziej; Harold A. Scheraga (Multiscale Model. Simul., 2006)

Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: All-atom molecular dynamics in implicit solvent. - Anna Jagielska; Harold A. Scheraga (J. Comput. Chem., 2007)

Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field. - Yi He; Yi Xiao; Adam Liwo; Harold A. Scheraga (J. Comput. Chem., 2009)

Performance of density functional models to reproduce observed 13Calpha chemical shifts of proteins in solution. - Jorge A. Vila; Héctor A. Baldoni; Harold A. Scheraga (J. Comput. Chem., 2009)

Global Optimization in Protein Folding. - Daniel R. Ripoll; Adam Liwo; Harold A. Scheraga (Encyclopedia of Optimization, 2009)

Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations. - Stanislaw Oldziej; Cezary Czaplewski; Adam Liwo; Harold A. Scheraga (BIBE, 2010)

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. - Urszula Kozlowska; Adam Liwo; Harold A. Scheraga (J. Comput. Chem., 2010)

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. - Urszula Kozlowska; Gia G. Maisuradze; Adam Liwo; Harold A. Scheraga (J. Comput. Chem., 2010)

Coarse-grained model of nucleic acid bases. - Maciej Maciejczyk; Aleksandar Spasic; Adam Liwo; Harold A. Scheraga (J. Comput. Chem., 2010)

CheShift-2: graphic validation of protein structures. - Osvaldo A. Martin; Jorge A. Vila; Harold A. Scheraga (Bioinform., 2012)

Factors affecting the computation of the 13C shielding in disaccharides. - Pablo G. Garay; Osvaldo A. Martin; Harold A. Scheraga; Jorge A. Vila (J. Comput. Chem., 2014)

Are accurate computations of the 13C′ shielding feasible at the DFT level of theory? - Jorge A. Vila; Yelena A. Arnautova; Osvaldo A. Martin; Harold A. Scheraga (J. Comput. Chem., 2014)

Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. - 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; et al. (Bioinform., 2016)

Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. - Pawel Krupa; Anna Halabis; Wioletta Zmudzinska; Stanislaw Oldziej; Harold A. Scheraga; Adam Liwo (J. Chem. Inf. Model., 2017)

A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields. - Adam K. Sieradzan; Artur Gieldon; Yanping Yin; Yi He; Harold A. Scheraga; Adam Liwo (J. Comput. Chem., 2018)

Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. - Pawel Krupa; Anna Halabis; Wioletta Zmudzinska; Stanislaw Oldziej; Harold A. Scheraga; Adam Liwo (J. Chem. Inf. Model., 2018)