% csauthors.net - beta - BibTeX bibliography of Harold A. Scheraga
@article{journals/bioinformatics/WeinerS89,
title = {A set of Macintosh computer programs for the design and analysis of synthetic genes.},
year = {1989},
journal = {Comput. Appl. Biosci.},
author = {{M. P. Weiner} and {Harold A. Scheraga}}
}
@article{journals/nar/WitmerFWKBGS91,
title = {U-3'-BCIP: a chromogenic substrate for the detection of RNase A in recombinant DNA expression systems.},
year = {1991},
journal = {Nucleic Acids Res.},
author = {{M. R. Witmer} and {C. M. Falcomer} and {M. P. Weiner} and {M. S. Kay} and {T. P. Begley} and {B. Ganem} and {Harold A. Scheraga}}
}
@article{journals/jcc/ParkNJS93,
title = {Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. III. Application to halogenated and aromatic molecules.},
year = {1993},
journal = {J. Comput. Chem.},
author = {{Je Myung Park} and {Kyoung Tai No} and {Mu Shik Jhon} and {Harold A. Scheraga}}
}
@article{journals/jcc/GibsonS94,
title = {A Rapid and Efficient Algorithm for Packing Polypeptide Chains by Energy Minimization.},
year = {1994},
journal = {J. Comput. Chem.},
author = {{Kenneth D. Gibson} and {Harold A. Scheraga}}
}
@article{journals/jcc/GibsonS94a,
title = {An Algorithm for Packing Regular Multistrand Polypeptide Structures by Energy Minimization.},
year = {1994},
journal = {J. Comput. Chem.},
author = {{Kenneth D. Gibson} and {Harold A. Scheraga}}
}
@inproceedings{conf/dimacs/KostrowickiS95,
title = {Some approaches to the multiple-minima problem in protein folding.},
year = {1995},
booktitle = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding},
author = {{Jaroslaw Kostrowicki} and {Harold A. Scheraga}},
publisher = {DIMACS/AMS},
booktitle = {Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, Proceedings of a DIMACS Workshop, USA, March 20-21, 1995}
}
@inproceedings{conf/sc/HaoS95,
title = {Computational Approach to the Statistical Mechanics of Protein Folding.},
year = {1995},
booktitle = {SC},
author = {{Ming-Hong Hao} and {Harold A. Scheraga}},
publisher = {ACM},
booktitle = {Proceedings Supercomputing '95, San Diego, CA, USA, December 4-8, 1995}
}
@article{journals/jcc/ParkKNJS95,
title = {Determination of Net Atomics Charges Using a Modified Partial Equalization or Orbital Electronegativity Method. IC. Application to Hypervalent Sulfur and Phosphorus-Containing Molecules.},
year = {1995},
journal = {J. Comput. Chem.},
author = {{Je Myung Park} and {Oh Young Kwon} and {Kyoung Tai No} and {Mu Shik Jhon} and {Harold A. Scheraga}}
}
@article{journals/jcc/RipollPGSL95,
title = {Implementation of the ECEPP Algorithm, the Monte Carlo Minimization Method, and the Electrostatically Driven Monte Carlo Method on the Kendall Square Research KSR1 Computer.},
year = {1995},
journal = {J. Comput. Chem.},
author = {{Daniel R. Ripoll} and {Marcia S. Pottle} and {Kenneth D. Gibson} and {Harold A. Scheraga} and {Adam Liwo}}
}
@article{journals/jgo/KostrowickiS95,
title = {Simple global minimization algorithm for one-variable rational functions.},
year = {1995},
journal = {J. Glob. Optim.},
author = {{Jaroslaw Kostrowicki} and {Harold A. Scheraga}}
}
@inproceedings{conf/hpcn/ODonnellHPRS96,
title = {Implementation of ECEPP-Based Programs on the IBM SP2 and the SGI Power Challenge Computers.},
year = {1996},
booktitle = {HPCN Europe},
author = {{Timothy J. O'Donnell} and {Steven Hotovy} and {Marcia S. Pottle} and {Daniel R. Ripoll} and {Harold A. Scheraga}},
publisher = {Springer},
booktitle = {High-Performance Computing and Networking, International Conference and Exhibition, HPCN Europe 1996, Brussels, Belgium, April 15-19, 1996, Proceedings}
}
@article{journals/jcc/AugspurgerS96,
title = {An efficient, differentiable hydration potential for peptides and proteins.},
year = {1996},
journal = {J. Comput. Chem.},
author = {{Joseph D. Augspurger} and {Harold A. Scheraga}}
}
@article{journals/jcc/ChengNS96,
title = {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.},
year = {1996},
journal = {J. Comput. Chem.},
author = {{Betty Cheng} and {Akbar Nayeem} and {Harold A. Scheraga}}
}
@article{journals/jcc/AugspurgerS97,
title = {An assessment of the accuracy of the RRIGS hydration potential: Comparison to solutions of the Poisson-Boltzmann equation.},
year = {1997},
journal = {J. Comput. Chem.},
author = {{Joseph D. Augspurger} and {Harold A. Scheraga}}
}
@article{journals/jcc/GibsonS97,
title = {Energy minimization of rigid-geometry polypeptides with exactly closed disulfide loops.},
year = {1997},
journal = {J. Comput. Chem.},
author = {{Kenneth D. Gibson} and {Harold A. Scheraga}}
}
@article{journals/jcc/LeeSR97,
title = {New optimization method for conformational energy calculations on polypeptides: Conformational space annealing.},
year = {1997},
journal = {J. Comput. Chem.},
author = {{Jooyoung Lee 002} and {Harold A. Scheraga} and {Shelly Rackovsky}}
}
@article{journals/jcc/LiwoOPWRS97,
title = {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.},
year = {1997},
journal = {J. Comput. Chem.},
author = {{Adam Liwo} and {Stanislaw Oldziej} and {Matthew R. Pincus} and {Ryszard J. Wawak} and {Shelly Rackovsky} and {Harold A. Scheraga}}
}
@article{journals/jcc/LiwoPWROS97,
title = {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.},
year = {1997},
journal = {J. Comput. Chem.},
author = {{Adam Liwo} and {Matthew R. Pincus} and {Ryszard J. Wawak} and {Shelly Rackovsky} and {Stanislaw Oldziej} and {Harold A. Scheraga}}
}
@article{journals/jcc/VorobjevS97,
title = {A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent.},
year = {1997},
journal = {J. Comput. Chem.},
author = {{Yury N. Vorobjev} and {Harold A. Scheraga}}
}
@article{journals/jcc/LiwoKCGOWRPS98,
title = {United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials.},
year = {1998},
journal = {J. Comput. Chem.},
author = {{Adam Liwo} and {Rajmund Kazmierkiewicz} and {Cezary Czaplewski} and {Malgorzata Groth} and {Stanislaw Oldziej} and {Ryszard J. Wawak} and {Shelly Rackovsky} and {Matthew R. Pincus} and {Harold A. Scheraga}}
}
@article{journals/jcc/OberlinS98,
title = {B-spline method for energy minimization in grid-based molecular mechanics calculations.},
year = {1998},
journal = {J. Comput. Chem.},
author = {{Daniel Oberlin} and {Harold A. Scheraga}}
}
@article{journals/jcc/TrossetS99,
title = {Flexible docking simulations: Scaled collective variable Monte Carlo minimization approach using Bezier splines, and comparison with a standard Monte Carlo algorithm.},
year = {1999},
journal = {J. Comput. Chem.},
author = {{Jean-Yves Trosset} and {Harold A. Scheraga}}
}
@article{journals/jcc/TrossetS99a,
title = {Prodock: Software package for protein modeling and docking.},
year = {1999},
journal = {J. Comput. Chem.},
author = {{Jean-Yves Trosset} and {Harold A. Scheraga}}
}
@article{journals/jcc/WedemeyerS99,
title = {Exact analytical loop closure in proteins using polynomial equations.},
year = {1999},
journal = {J. Comput. Chem.},
author = {{William J. Wedemeyer} and {Harold A. Scheraga}}
}
@article{journals/jgo/ScheragaLPYLR99,
title = {Surmounting the Multiple-Minima Problem in Protein Folding.},
year = {1999},
journal = {J. Glob. Optim.},
author = {{Harold A. Scheraga} and {Jooyoung Lee 002} and {Jaroslaw Pillardy} and {Yuan-Jie Ye} and {Adam Liwo} and {Daniel R. Ripoll}}
}
@inproceedings{conf/recomb/LiwoPCLRGRKWOS00,
title = {UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody terms.},
year = {2000},
booktitle = {RECOMB},
author = {{Adam Liwo} and {Jaroslaw Pillardy} and {Cezary Czaplewski} and {Jooyoung Lee 002} and {Daniel R. Ripoll} and {Malgorzata Groth} and {Sylwia Rodziewicz-Motowidlo} and {Rajmund Kazmierkiewicz} and {Ryszard J. Wawak} and {Stanislaw Oldziej} and {Harold A. Scheraga}},
publisher = {ACM},
booktitle = {Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, RECOMB 2000, Tokyo, Japan, April 8-11, 2000}
}
@inproceedings{conf/psb/SaundersGS02,
title = {Ab Initio Folding of Multiple-Chain Proteins.},
year = {2002},
booktitle = {Pacific Symposium on Biocomputing},
author = {{J. A. Saunders} and {Kenneth D. Gibson} and {Harold A. Scheraga}},
booktitle = {Proceedings of the 7th Pacific Symposium on Biocomputing, PSB 2002, Lihue, Hawaii, USA, January 3-7, 2002}
}
@article{journals/jcc/KamierkiewiczLS02,
title = {Energy-based reconstruction of a protein backbone from its -carbon trace by a Monte-Carlo method.},
year = {2002},
journal = {J. Comput. Chem.},
author = {{Rajmund Kazmierkiewicz} and {Adam Liwo} and {Harold A. Scheraga}}
}
@article{journals/jcc/ScheragaPLLCRWA02,
title = {Evolution of physics-based methodology for exploring the conformational energy landscape of proteins.},
year = {2002},
journal = {J. Comput. Chem.},
author = {{Harold A. Scheraga} and {Jaroslaw Pillardy} and {Adam Liwo} and {Jooyoung Lee 002} and {Cezary Czaplewski} and {Daniel R. Ripoll} and {William J. Wedemeyer} and {Yelena A. Arnautova}}
}
@article{journals/jcc/NaniasCOCS05,
title = {Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC.},
year = {2005},
journal = {J. Comput. Chem.},
author = {{Marian Nanias} and {Maurizio Chinchio} and {Stanislaw Oldziej} and {Cezary Czaplewski} and {Harold A. Scheraga}}
}
@article{journals/mmas/ChinchioCOS06,
title = {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.},
year = {2006},
journal = {Multiscale Model. Simul.},
author = {{Maurizio Chinchio} and {Cezary Czaplewski} and {Stanislaw Oldziej} and {Harold A. Scheraga}}
}
@article{journals/jcc/JagielskaS07,
title = {Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: All-atom molecular dynamics in implicit solvent.},
year = {2007},
journal = {J. Comput. Chem.},
author = {{Anna Jagielska} and {Harold A. Scheraga}}
}
@article{journals/jcc/HeXLS09,
title = {Exploring the parameter space of the coarse-grained UNRES force field by random search: Selecting a transferable medium-resolution force field.},
year = {2009},
journal = {J. Comput. Chem.},
author = {{Yi He} and {Yi Xiao} and {Adam Liwo} and {Harold A. Scheraga}}
}
@article{journals/jcc/VilaBS09,
title = {Performance of density functional models to reproduce observed 13Calpha chemical shifts of proteins in solution.},
year = {2009},
journal = {J. Comput. Chem.},
author = {{Jorge A. Vila} and {Héctor A. Baldoni} and {Harold A. Scheraga}}
}
@incollection{reference/opt/RipollLS09,
title = {Global Optimization in Protein Folding.},
year = {2009},
booktitle = {Encyclopedia of Optimization},
author = {{Daniel R. Ripoll} and {Adam Liwo} and {Harold A. Scheraga}},
publisher = {Springer},
booktitle = {Encyclopedia of Optimization, Second Edition}
}
@inproceedings{conf/bibe/OldziejCLS10,
title = {Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations.},
year = {2010},
booktitle = {BIBE},
author = {{Stanislaw Oldziej} and {Cezary Czaplewski} and {Adam Liwo} and {Harold A. Scheraga}},
publisher = {IEEE Computer Society},
booktitle = {10th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2010, Philadelphia, Pennsylvania, USA, May 31-June 3 2010}
}
@article{journals/jcc/KozlowskaLS10,
title = {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.},
year = {2010},
journal = {J. Comput. Chem.},
author = {{Urszula Kozlowska} and {Adam Liwo} and {Harold A. Scheraga}}
}
@article{journals/jcc/KozlowskaMLS10,
title = {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.},
year = {2010},
journal = {J. Comput. Chem.},
author = {{Urszula Kozlowska} and {Gia G. Maisuradze} and {Adam Liwo} and {Harold A. Scheraga}}
}
@article{journals/jcc/MaciejczykSLS10,
title = {Coarse-grained model of nucleic acid bases.},
year = {2010},
journal = {J. Comput. Chem.},
author = {{Maciej Maciejczyk} and {Aleksandar Spasic} and {Adam Liwo} and {Harold A. Scheraga}}
}
@article{journals/bioinformatics/MartinVS12,
title = {CheShift-2: graphic validation of protein structures.},
year = {2012},
journal = {Bioinform.},
author = {{Osvaldo A. Martin} and {Jorge A. Vila} and {Harold A. Scheraga}}
}
@article{journals/jcc/GarayMSV14,
title = {Factors affecting the computation of the 13C shielding in disaccharides.},
year = {2014},
journal = {J. Comput. Chem.},
author = {{Pablo G. Garay} and {Osvaldo A. Martin} and {Harold A. Scheraga} and {Jorge A. Vila}}
}
@article{journals/jcc/VilaAMS14,
title = {Are accurate computations of the 13C′ shielding feasible at the DFT level of theory?},
year = {2014},
journal = {J. Comput. Chem.},
author = {{Jorge A. Vila} and {Yelena A. Arnautova} and {Osvaldo A. Martin} and {Harold A. Scheraga}}
}
@article{journals/bioinformatics/KrupaMWYHSGLKSS16,
title = {Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.},
year = {2016},
journal = {Bioinform.},
author = {{Pawel Krupa} and {Magdalena A. Mozolewska} and {Marta Wisniewska} and {Yanping Yin} and {Yi He} and {Adam K. Sieradzan} and {Robert Ganzynkowicz} and {Agnieszka G. Lipska} and {Agnieszka S. Karczynska} and {Magdalena Slusarz} and {Rafal Slusarz} and {Artur Gieldon} and {Cezary Czaplewski} and {Dawid Jagiela} and {Bartlomiej Zaborowski} and {Harold A. Scheraga} and {Adam Liwo}}
}
@article{journals/jcisd/KrupaHZOSL17,
title = {Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics.},
year = {2017},
month = {September},
journal = {J. Chem. Inf. Model.},
author = {{Pawel Krupa} and {Anna Halabis} and {Wioletta Zmudzinska} and {Stanislaw Oldziej} and {Harold A. Scheraga} and {Adam Liwo}}
}
@article{journals/jcc/SieradzanGYHSL18,
title = {A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields.},
year = {2018},
journal = {J. Comput. Chem.},
author = {{Adam K. Sieradzan} and {Artur Gieldon} and {Yanping Yin} and {Yi He} and {Harold A. Scheraga} and {Adam Liwo}}
}
@article{journals/jcisd/KrupaHZOSL18,
title = {Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics.},
year = {2018},
journal = {J. Chem. Inf. Model.},
author = {{Pawel Krupa} and {Anna Halabis} and {Wioletta Zmudzinska} and {Stanislaw Oldziej} and {Harold A. Scheraga} and {Adam Liwo}}
}