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Harold A. Scheraga
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2010 – 2019
- 2018
- [j39]Adam K. Sieradzan
, Artur Gieldon
A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields. J. Comput. Chem. 39(28): 2360-2370 (2018) - [j38]Pawel Krupa, Anna Halabis, Wioletta Zmudzinska, Stanislaw Oldziej, Harold A. Scheraga
Correction to Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. J. Chem. Inf. Model. 58(1): 206 (2018) - 2017
- [j37]Pawel Krupa
Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. J. Chem. Inf. Model. 57(9): 2364-2377 (2017) - 2016
- [j36]Pawel Krupa
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. Bioinform. 32(21): 3270-3278 (2016) - 2014
- [j35]Jorge A. Vila
Are accurate computations of the 13C′ shielding feasible at the DFT level of theory? J. Comput. Chem. 35(4): 309-312 (2014) - [j34]Pablo G. Garay
Factors affecting the computation of the 13C shielding in disaccharides. J. Comput. Chem. 35(25): 1854-1864 (2014) - 2012
- [j33]Osvaldo A. Martin
CheShift-2: graphic validation of protein structures. Bioinform. 28(11): 1538-1539 (2012) - 2010
- [j32]Urszula Kozlowska, Adam Liwo
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): 1143-1153 (2010) - [j31]Urszula Kozlowska, Gia G. Maisuradze, Adam Liwo
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): 1154-1167 (2010) - [j30]Maciej Maciejczyk
Coarse-grained model of nucleic acid bases. J. Comput. Chem. 31(8): 1644-1655 (2010) - [c6]Stanislaw Oldziej
Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations. BIBE 2010: 263-266
2000 – 2009
- 2009
- [j29]Jorge A. Vila
Performance of density functional models to reproduce observed 13Calpha chemical shifts of proteins in solution. J. Comput. Chem. 30(6): 884-892 (2009) - [j28]Yi He, Yi Xiao, Adam Liwo
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): 2127-2135 (2009) - [r1]Daniel R. Ripoll, Adam Liwo
Global Optimization in Protein Folding. Encyclopedia of Optimization 2009: 1392-1411 - 2007
- [j27]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): 1068-1082 (2007) - 2006
- [j26]Maurizio Chinchio, Cezary Czaplewski
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): 1175-1195 (2006) - 2005
- [j25]Marian Nanias, Maurizio Chinchio, Stanislaw Oldziej
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): 1472-1486 (2005) - 2002
- [j24]Harold A. Scheraga, Jaroslaw Pillardy, Adam Liwo
Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. J. Comput. Chem. 23(1): 28-34 (2002) - [j23]Rajmund Kazmierkiewicz, Adam Liwo
Energy-based reconstruction of a protein backbone from its -carbon trace by a Monte-Carlo method. J. Comput. Chem. 23(7): 715-723 (2002) - [c5]J. A. Saunders, Kenneth D. Gibson, Harold A. Scheraga:
Ab Initio Folding of Multiple-Chain Proteins. Pacific Symposium on Biocomputing 2002: 601-612 - 2000
- [c4]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
1990 – 1999
- 1999
- [j22]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): 244-252 (1999) - [j21]Jean-Yves Trosset, Harold A. Scheraga:
Prodock: Software package for protein modeling and docking. J. Comput. Chem. 20(4): 412-427 (1999) - [j20]William J. Wedemeyer, Harold A. Scheraga:
Exact analytical loop closure in proteins using polynomial equations. J. Comput. Chem. 20(8): 819-844 (1999) - [j19]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): 235-260 (1999) - 1998
- [j18]Daniel Oberlin, Harold A. Scheraga:
B-spline method for energy minimization in grid-based molecular mechanics calculations. J. Comput. Chem. 19(1): 71-85 (1998) - [j17]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): 259-276 (1998) - 1997
- [j16]Kenneth D. Gibson, Harold A. Scheraga:
Energy minimization of rigid-geometry polypeptides with exactly closed disulfide loops. J. Comput. Chem. 18(3): 403-415 (1997) - [j15]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): 569-583 (1997) - [j14]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): 849-873 (1997) - [j13]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): 874-887 (1997) - [j12]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): 1072-1078 (1997) - [j11]Jooyoung Lee, Harold A. Scheraga, Shelly Rackovsky:
New optimization method for conformational energy calculations on polypeptides: Conformational space annealing. J. Comput. Chem. 18(9): 1222-1232 (1997) - 1996
- [j10]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): 1453-1480 (1996) - [j9]Joseph D. Augspurger, Harold A. Scheraga:
An efficient, differentiable hydration potential for peptides and proteins. J. Comput. Chem. 17(13): 1549-1558 (1996) - [c3]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 - 1995
- [j8]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): 1011-1027 (1995) - [j7]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): 1153-1163 (1995) - [j6]Jaroslaw Kostrowicki, Harold A. Scheraga:
Simple global minimization algorithm for one-variable rational functions. J. Glob. Optim. 6(3): 293-311 (1995) - [c2]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: 123-132 - [c1]Ming-Hong Hao, Harold A. Scheraga:
Computational Approach to the Statistical Mechanics of Protein Folding. SC 1995: 21 - 1994
- [j5]Kenneth D. Gibson, Harold A. Scheraga:
A Rapid and Efficient Algorithm for Packing Polypeptide Chains by Energy Minimization. J. Comput. Chem. 15(12): 1403-1413 (1994) - [j4]Kenneth D. Gibson, Harold A. Scheraga:
An Algorithm for Packing Regular Multistrand Polypeptide Structures by Energy Minimization. J. Comput. Chem. 15(12): 1414-1428 (1994) - 1993
- [j3]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): 1482-1490 (1993) - 1991
- [j2]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): 1-4 (1991)
1980 – 1989
- 1989
- [j1]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): 191-198 (1989)
Coauthor Index
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