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1
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0033610078
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Global optimization of clusters, crystals and biomolecules
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Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions and intrinsic torsional potential for the naturally occurring aminoacids
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33845550595
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Némethy, G.1
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27244454740
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Intermolecular potentials from crystal data. VI. Determination of empirical potentials for O-H⋯O-C hydrogen bonds from packing configurations
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5
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0001731773
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Energy parameters in polypeptides. X. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
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Némethy, G., Gibson, K.D., Palmer, K.A., Yoon, C.N., Paterlini, G., Zagari, A., Rumsey, S. and Scheraga, H.A. (1992), Energy parameters in polypeptides. X. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides, J. Phys. Chem. 96: 6472-6484.
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6
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0027524668
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Calculation of protein backbone geometry from α-carbon coordinates based on peptide-group dipole alignment
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Liwo, A., Pincus, M.R., Wawak, R.J., Rackovsky, S. and Scheraga, H.A. (1993), Calculation of protein backbone geometry from α-carbon coordinates based on peptide-group dipole alignment, Protein Science 2: 1697-1714.
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7
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0027435091
-
Prediction of protein conformation on the basis of a search for compact structures; test on avian pancreatic polypeptide
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Liwo, A., Pincus, M.R., Wawak, R.J., Rackovsky, S. and Scheraga, H.A. (1993), Prediction of protein conformation on the basis of a search for compact structures; test on avian pancreatic polypeptide, Protein Science 2: 1715-1731.
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8
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-
0000095892
-
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
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Liwo, A., Oldziej, S., Pincus, M.R., Wawak, R.J., Rackovsky, S. and Scheraga, H.A. (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, J. Comput. Chem. 18: 849-873.
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9
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0000095890
-
A united-residue force field for off-lattice protein-structure simulations. II: Parameterization of short-range interactions and determination of the weights of energy terms by Z-score optimization
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Liwo, A., Pincus, M.R., Wawak, R.J., Rackovsky, S., Oldziej, S. and Scheraga, H.A. (1997), A united-residue force field for off-lattice protein-structure simulations. II: Parameterization of short-range interactions and determination of the weights of energy terms by Z-score optimization, J. Comput. Chem. 18: 874-887.
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10
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0001181898
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A united-residue force field for off-lattice protein-structure simulations. III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials
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Liwo, A., Kazmierkiewicz, R., Czaplewski, C., Groth, M., Oldziej, S., Wawak, R.J., Rackovsky, S., Pincus, M.R. and Scheraga, H.A. (1998), A 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: 259-276.
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0347525711
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Prediction of protein conformation
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0042153813
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Conformational energy calculations of the effects of sequence variations on the conformations of two tetrapeptides
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Simon, I.1
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0020170122
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Calculation of the three-dimensional structure of the membrane-bound portion of melittin from its amino acid sequence
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Recent progress in the theoretical treatment of protein folding
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0021813809
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Use of buildup and energy-minimization procedures to compute low-energy structures of the backbone of enkephalin
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Revised algorithms for the build-up procedure for predicting protein conformations by energy minimization
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0001298333
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Computed conformational states of the 20 naturally occurring amino acid residues and of the prototype residue α-aminobutyric acid
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0017435119
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Conformational analysis of the twenty naturally occurring amino acid residues using ECEPP
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19
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0023921186
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Calculation of protein conformation by the build-up procedure. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data
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Variable-target-function and build-up procedures for the calculation of protein conformation. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data
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Vásquez, M. and Scheraga, H.A. (1988), Variable-target-function and build-up procedures for the calculation of protein conformation. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data, J. Biomol. Struct. & Dyn. 5: 757-784.
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0016579644
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Use of a symmetry condition to compute the conformation of gramicidin S
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Hydrogen bonding involving the ornithine side chain of gramicidin S
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Calculation of the structures of collagen models. Role of interchain interactions in determining the triple-helical coiled-coil conformation. 1. Poly(glycyl-prolyl-prolyl)
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Calculation of the structures of collagen models. Role of interchain interactions in determining the triple-helical coiled-coil conformation. 2. Poly(glycyl-prolyl-hydroxyprolyl)
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Calculation of the structures of collagen models. Role of interchain interactions in determining the triple-helical coiled-coil conformation. 3. Poly(glycyl-prolyl-alanyl)
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Structural patterns in globular proteins
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The α-helix as an electric macro-dipole
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Energetic approach to the packing of α-helices. 1. Equivalent helices
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The role of the α-helix dipole in protein function and structure
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On the multiple-minima problem in the conformational analysis of polypeptides. I. Backbone degrees of freedom for a perturbed α-helix
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0026005891
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On the multiple-minima problem in the conformational analysis of polypeptides. V. Application of the self-consistent electrostatic field and the electrostatically driven Monte Carlo methods to bovine pancreatic trypsin inhibitor
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Monte Carlo-minimization approach to the multiple-minima problem in protein folding
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Structure and free energy of complex thermodynamic systems
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Equation of state calculations by fast computing machines
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Computer simulation of the conformational properties of oligopeptides. Comparison of theoretical methods and analysis of experimental results
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Evolution and stability of polypeptide chain conformation: A simulation study
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40
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0022105875
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Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. I. Backbone structure of enkephalin
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Algorithm 611. Subroutines for unconstrained minimization using a model/trust-region approach
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0024066560
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On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method-tests on poly(L-alanine)
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New developments of the electrostatically driven Monte Carlo method - Test on the membrane bound portion of melittin
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Biopolymers
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0030051535
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Exploration of the conformational space of oxytocin and arginine-vasopressin using the electrostatically-driven Monte Carlo and molecular dynamics methods
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Liwo, A., Tempczyk, A., Ołdziej, S., Shenderovich, M.D., Hruby, V.J., Talluri, S., Ciarkowski, J., Kasprzykowski, F., Łankiewicz, L. and Grzonka, Z. (1996), Exploration of the conformational space of oxytocin and arginine-vasopressin using the electrostatically-driven Monte Carlo and molecular dynamics methods, Biopolymers 38: 157-175.
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46
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0026103603
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The electrostatically driven Monte Carlo method: Application to conformational analysis of decaglycine
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