(Q33803957)

29 July 2017

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title

Towards understanding the mechanisms of molecular recognition by computer simulations of ligand-protein interactions (English)

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29 July 2017

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11

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ORCID Public Data File 2021

29 July 2017

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author name string

Verkhivker GM

1

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29 July 2017

Rejto PA

2

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29 July 2017

Bouzida D

3

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29 July 2017

Arthurs S

4

1 reference

29 July 2017

Colson AB

5

1 reference

29 July 2017

Freer ST

6

1 reference

29 July 2017

Gehlhaar DK

7

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29 July 2017

Larson V

8

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29 July 2017

Luty BA

9

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29 July 2017

Marrone T

10

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29 July 2017

publication date

1 November 1999

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Journal of Molecular Recognition

29 July 2017

published in

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29 July 2017

volume

12

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29 July 2017

issue

6

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29 July 2017

page(s)

371-389

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Specific nucleus as the transition state for protein folding: evidence from the lattice model.

29 July 2017

cites work

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Impact of local and non-local interactions on thermodynamics and kinetics of protein folding

21 January 2018

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21 January 2018

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21 January 2018

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21 January 2018

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The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure

21 January 2018

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21 January 2018

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21 January 2018

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Funnels, pathways, and the energy landscape of protein folding: a synthesis

21 January 2018

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21 January 2018

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Kinetics and thermodynamics of folding in model proteins

21 January 2018

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Protein-protein recognition analyzed by docking simulation.

21 January 2018

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A hot spot of binding energy in a hormone-receptor interface

21 January 2018

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De novo protein design: fully automated sequence selection

21 January 2018

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Dominant forces in protein folding

21 January 2018

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From Levinthal to pathways to funnels

21 January 2018

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Principles of protein folding--a perspective from simple exact models.

21 January 2018

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Molecular dynamics simulation of the docking of substrates to proteins.

21 January 2018

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Discrete molecular dynamics studies of the folding of a protein-like model.

21 January 2018

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Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

21 January 2018

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On constructing folding heteropolymers

21 January 2018

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Co-operativity in protein-protein association. The structure and stability of the actin filament

21 January 2018

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Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications

21 January 2018

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Nucleation mechanisms in protein folding

21 January 2018

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The Energy Landscapes and Motions of Proteins

21 January 2018

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Predicting molecular interactions and inducible complementarity: fragment docking of Fab-peptide complexes.

21 January 2018

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Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming

21 January 2018

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The statistical-thermodynamic basis for computation of binding affinities: a critical review

21 January 2018

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Theoretical Studies of Protein Folding

21 January 2018

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Optimal protein-folding codes from spin-glass theory

21 January 2018

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Automated docking of substrates to proteins by simulated annealing

21 January 2018

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Molecular docking towards drug discovery

21 January 2018

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Thermodynamics of protein folding: a statistical mechanical study of a small all-beta protein

21 January 2018

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The nucleation-collapse mechanism in protein folding: evidence for the non-uniqueness of the folding nucleus

21 January 2018

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Exploring the folding free energy surface of a three-helix bundle protein

21 January 2018

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Evolution-like selection of fast-folding model proteins

21 January 2018

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Characteristic temperatures of folding of a small peptide

21 January 2018

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A multiple-start Monte Carlo docking method.

21 January 2018

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Calculation of the free energy of association for protein complexes

21 January 2018

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A continuum model for protein-protein interactions: application to the docking problem.

21 January 2018

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Structure-derived potentials and protein simulations

21 January 2018

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"Soft docking": matching of molecular surface cubes

21 January 2018

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Docking small-molecule ligands into active sites

21 January 2018

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Development and validation of a genetic algorithm for flexible docking

21 January 2018

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The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

21 January 2018

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Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques

21 January 2018

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Binding to protein targets of peptidic leads discovered by phage display: crystal structures of streptavidin-bound linear and cyclic peptide ligands containing the HPQ sequence

21 January 2018

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Kinetic traps in lysozyme folding

21 January 2018

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Lattice models for proteins reveal multiple folding nuclei for nucleation-collapse mechanism

21 January 2018

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Molecular docking to ensembles of protein structures

21 January 2018

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Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme.

21 January 2018

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Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures.

21 January 2018

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Structure-based strategies for drug design and discovery

21 January 2018

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"New view" of protein folding reconciled with the old through multiple unfolding simulations.

21 January 2018

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Ligand docking to proteins with discrete side-chain flexibility.

21 January 2018

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Protein folding funnels: a kinetic approach to the sequence-structure relationship

21 January 2018

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Molecular surface representations by sparse critical points

21 January 2018

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Ligand—protein docking and rational drug design

21 January 2018

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Contribution of hydration to protein folding thermodynamics. I. The enthalpy of hydration

21 January 2018

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Analogous inhibitors of elastase do not always bind analogously

21 January 2018

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How evolution makes proteins fold quickly

21 January 2018

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Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.

21 January 2018

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Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse, points in docking

21 January 2018

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Toward an outline of the topography of a realistic protein-folding funnel

21 January 2018

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Protein folding funnels: the nature of the transition state ensemble

21 January 2018

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Flexible ligand docking using a genetic algorithm.

21 January 2018

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Is the molten globule a third phase of proteins?

21 January 2018

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Folding pathway of a lattice model for proteins

21 January 2018

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Pathways for protein folding: is a new view needed?

21 January 2018

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Intermediate states in protein folding

21 January 2018

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Contribution of hydration to protein folding thermodynamics. II. The entropy and Gibbs energy of hydration

21 January 2018

1 reference

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A fast flexible docking method using an incremental construction algorithm.

21 January 2018

1 reference

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Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention.

21 January 2018

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Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors.

21 January 2018

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Flexible Docking and Design

21 January 2018

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Kinetics of protein folding. A lattice model study of the requirements for folding to the native state.

21 January 2018

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21 January 2018

How does a protein fold?

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Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization

21 January 2018

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Structural consensus in ligand-protein docking identifies recognition peptide motifs that bind streptavidin

21 January 2018

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Protein design: a perspective from simple tractable models

21 January 2018

1 reference

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Engineering of stable and fast-folding sequences of model proteins

21 January 2018

1 reference

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Protein docking and complementarity

21 January 2018

1 reference

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Structure-based discovery of inhibitors of thymidylate synthase

21 January 2018

1 reference

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Molecular docking using surface complementarity.

21 January 2018

1 reference

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Coupling of local folding to site-specific binding of proteins to DNA

21 January 2018

1 reference

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Molecular recognition analyzed by docking simulations: the aspartate receptor and isocitrate dehydrogenase from Escherichia coli

21 January 2018

1 reference

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CombiDOCK: structure-based combinatorial docking and library design

21 January 2018

1 reference

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A new method for predicting binding free energy between receptor and ligand.

21 January 2018

1 reference

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Detailed ab initio prediction of lysozyme–antibody complex with 1.6 Å accuracy

21 January 2018

1 reference

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Empirical potentials and functions for protein folding and binding.

21 January 2018

1 reference

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Hydrophobic docking: a proposed enhancement to molecular recognition techniques.

21 January 2018

1 reference

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Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex

21 January 2018

1 reference

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Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin

21 January 2018

1 reference

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A mean field model of ligand-protein interactions: implications for the structural assessment of human immunodeficiency virus type 1 protease complexes and receptor-specific binding

21 January 2018

1 reference

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Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity.

21 January 2018

1 reference

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Exploring the energy landscapes of molecular recognition by a genetic algorithm: analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes

21 January 2018

1 reference

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A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design

21 January 2018

1 reference

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New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen docking

21 January 2018

1 reference

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Crystal structure and ligand-binding studies of a screened peptide complexed with streptavidin

21 January 2018

1 reference

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Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites.

21 January 2018

1 reference

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Prediction of protein complexes using empirical free energy functions

21 January 2018

1 reference

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Empirical free energy calculation: comparison to calorimetric data

21 January 2018

1 reference

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A comparison of heuristic search algorithms for molecular docking.

21 January 2018

1 reference

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Distance-constrained molecular docking by simulated annealing.

21 January 2018

1 reference

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Determination of atomic desolvation energies from the structures of crystallized proteins.

21 January 2018

1 reference

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Folding thermodynamics of a model three-helix-bundle protein.

21 January 2018

1 reference

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THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method

21 January 2018

1 reference

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Decomposition of the Free Energy of a System in Terms of Specific Interactions

21 January 2018

1 reference

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The Structure of the Transition State for Folding of Chymotrypsin Inhibitor 2 Analysed by Protein Engineering Methods: Evidence for a Nucleation-condensation Mechanism for Protein Folding

21 January 2018

1 reference

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Conserved residues and the mechanism of protein folding

21 January 2018

1 reference

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Folding and misfolding of designed proteinlike chains with mutations

21 January 2018

1 reference

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First-principles calculation of the folding free energy of a three-helix bundle protein

21 January 2018

1 reference

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Efficient Monte Carlo methods for the computer simulation of biological molecules

21 January 2018

1 reference

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A shape- and chemistry-based docking method and its use in the design of HIV-1 protease inhibitors

21 January 2018

1 reference

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New Monte Carlo technique for studying phase transitions

21 January 2018

1 reference

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Optimized Monte Carlo data analysis

21 January 2018

1 reference

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21 January 2018

Complexity in proteins

1 reference

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Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein

21 January 2018

1 reference

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Is burst hydrophobic collapse necessary for protein folding?

21 January 2018

1 reference

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Discovering high-affinity ligands for proteins

21 January 2018

1 reference

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Refolding and association of oligomeric proteins

21 January 2018

1 reference

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Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities

21 January 2018

1 reference

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21 January 2018

1 reference

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Quantifying biological specificity: the statistical mechanics of molecular recognition

21 January 2018

1 reference

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Criterion that determines the foldability of proteins

21 January 2018

1 reference

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Factors governing the foldability of proteins

21 January 2018

1 reference

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Cooperativity in protein folding: from lattice models with sidechains to real proteins

21 January 2018

1 reference

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Multidimensional free-energy calculations using the weighted histogram analysis method

21 January 2018

1 reference

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Hydration effects in protein unfolding

21 January 2018

1 reference

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DREIDING: a generic force field for molecular simulations

21 January 2018

1 reference

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Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model

21 January 2018

1 reference

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Proteins with selected sequences fold into unique native conformation

21 January 2018

1 reference

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Theoretical studies of protein-folding thermodynamics and kinetics

21 January 2018

1 reference

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Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of a replica approach

21 January 2018

1 reference

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Protein folding bottlenecks: A lattice Monte Carlo simulation

21 January 2018

1 reference

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Calculations on folding of segment B1 of streptococcal protein G

21 January 2018

1 reference

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Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2F%28SICI%291099-1352%28199911%2F12%2912%3A6%3C371%3A%3AAID-JMR479%3E3.0.CO%3B2-O

10.1002/(SICI)1099-1352(199911/12)12:6<371::AID-JMR479>3.0.CO;2-O

21 January 2018

Identifiers

DOI

1 reference

29 July 2017

1 reference