Harold A. Scheraga

According to our database1, Harold A. Scheraga authored at least 44 papers between 1989 and 2018.

Collaborative distances:
  • Dijkstra number2 of five.
  • Erdős number3 of four.

Timeline

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PhD thesis 
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Bibliography

2018
A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields.
Journal of Computational Chemistry, 2018

2016
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.
Bioinformatics, 2016

2014
Are accurate computations of the 13C′ shielding feasible at the DFT level of theory?
Journal of Computational Chemistry, 2014

Factors affecting the computation of the 13C shielding in disaccharides.
Journal of Computational Chemistry, 2014

2012
CheShift-2: graphic validation of protein structures.
Bioinformatics, 2012

2010
Coarse-grained model of nucleic acid bases.
Journal of Computational Chemistry, 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.
Journal of Computational Chemistry, 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.
Journal of Computational Chemistry, 2010

Towards Temperature Dependent Coarse-grained Potential of Side-chain Interactions for Protein Folding Simulations.
Proceedings of the 10th IEEE International Conference on Bioinformatics and Bioengineering, 2010

2009
Global Optimization in Protein Folding.
Proceedings of the Encyclopedia of Optimization, Second Edition, 2009

Performance of density functional models to reproduce observed 13Calpha chemical shifts of proteins in solution.
Journal of Computational Chemistry, 2009

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, 2009

2007
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, 2007

2006
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 Modeling & Simulation, 2006

2005
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, 2005

2002
Evolution of physics-based methodology for exploring the conformational energy landscape of proteins.
Journal of Computational Chemistry, 2002

Energy-based reconstruction of a protein backbone from its -carbon trace by a Monte-Carlo method.
Journal of Computational Chemistry, 2002

Ab Initio Folding of Multiple-Chain Proteins.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

2000
UNRES: a united-residue force field for energy-based prediction of protein structure - orgin and significance of multibody terms.
Proceedings of the Fourth Annual International Conference on Computational Molecular Biology, 2000

1999
Surmounting the Multiple-Minima Problem in Protein Folding.
J. Global Optimization, 1999

Exact analytical loop closure in proteins using polynomial equations.
Journal of Computational Chemistry, 1999

Prodock: Software package for protein modeling and docking.
Journal of Computational Chemistry, 1999

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, 1999

1998
B-spline method for energy minimization in grid-based molecular mechanics calculations.
Journal of Computational Chemistry, 1998

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, 1998

1997
A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent.
Journal of Computational Chemistry, 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.
Journal of Computational Chemistry, 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.
Journal of Computational Chemistry, 1997

New optimization method for conformational energy calculations on polypeptides: Conformational space annealing.
Journal of Computational Chemistry, 1997

Energy minimization of rigid-geometry polypeptides with exactly closed disulfide loops.
Journal of Computational Chemistry, 1997

An assessment of the accuracy of the RRIGS hydration potential: Comparison to solutions of the Poisson-Boltzmann equation.
Journal of Computational Chemistry, 1997

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.
Journal of Computational Chemistry, 1996

An efficient, differentiable hydration potential for peptides and proteins.
Journal of Computational Chemistry, 1996

Implementation of ECEPP-Based Programs on the IBM SP2 and the SGI Power Challenge Computers.
Proceedings of the High-Performance Computing and Networking, 1996

1995
Simple global minimization algorithm for one-variable rational functions.
J. Global Optimization, 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.
Journal of Computational Chemistry, 1995

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, 1995

Computational Approach to the Statistical Mechanics of Protein Folding.
Proceedings of the Proceedings Supercomputing '95, San Diego, CA, USA, December 4-8, 1995, 1995

Some approaches to the multiple-minima problem in protein folding.
Proceedings of the Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, 1995

1994
An Algorithm for Packing Regular Multistrand Polypeptide Structures by Energy Minimization.
Journal of Computational Chemistry, 1994

A Rapid and Efficient Algorithm for Packing Polypeptide Chains by Energy Minimization.
Journal of Computational Chemistry, 1994

1993
Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. III. Application to halogenated and aromatic molecules.
Journal of Computational Chemistry, 1993

1991
U-3'-BCIP: a chromogenic substrate for the detection of RNase A in recombinant DNA expression systems.
Nucleic Acids Research, 1991

1989
A set of Macintosh computer programs for the design and analysis of synthetic genes.
Computer Applications in the Biosciences, 1989


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