Monte carlo simulations of protein folding. I. Lattice model and interaction scheme
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Summary
A new hierarchical method for the simulation of the protein folding process and the de novo prediction of protein three‐dimensional structure is proposed, which employs lattice discretizations of increasing geometrical resolution and a single ball representation of side chain rotamers.
- Type
- article
- Published
- 1994-04-01
- Cited by
- 276
- References
- 58
- OpenAlex
- https://openalex.org/W2076488922
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:15421872
Keywords
Monte Carlo method, Globular protein, Statistical physics, Lattice (music), Protein folding
References
- The Protein Data Bank: a computer-based archival file for macromolecular structures.
- Are there pathways for protein folding
- Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme.
- Protein folding: Current Opinion in Structural Biology 1991, 1:224–229
- An analysis of incorrectly folded protein models. Implications for structure predictions.
- How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin.
- Radial locations of amino acid residues in a globular protein: correlation with the sequence.
- Profile analysis: detection of distantly related proteins.
- Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics
- The Protein Data Bank: a computer-based archival file for macromolecular structures.
- Sequence-structure matching in globular proteins: application to supersecondary and tertiary structure determination.
- On the multiple-minima problem in the conformational analysis of molecules: deformation of the potential energy hypersurface by the diffusion equation method
- Folding proteins: finding a needle in a haystack
- Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin.
- Monte Carlo studies on the long time dynamic properties of dense cubic lattice multichain systems. I. The homopolymeric melt
- Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features
- Metal ion-dependent modulation of the dynamics of a designed protein.
- Detection of native‐like models for amino acid sequences of unknown three‐dimensional structure in a data base of known protein conformations
- De novo and inverse folding predictions of protein structure and dynamics
- Molecular simulations of peptide and protein unfolding: in quest of a molten globule
Cited by
- What should the Z‐score of native protein structures be?
- Scoring functions for ab initio protein structure prediction.
- Protein refolding versus aggregation: computer simulations on an intermediate-resolution protein model.
- Computational simulations of protein folding to engineer amino acid sequences to encourage desired supersecondary structure formation.
- Monte Carlo Simulations of Protein Folding
- Ab initio modeling
- Self-organizing dynamics in protein folding.
- Folding a 20 amino acid αβ peptide with the diffusion process-controlled Monte Carlo method
- Identifying importance of amino acids for protein folding from crystal structures.
- Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus
- Protein Conformation of a Lattice Model Using Tabu Search
- Monte Carlo studies of the mechanical properties of biopolymers
- The energy landscape theory of protein folding: insights into folding mechanisms and scenarios.
- Determination of optimal effective interactions between amino acids in globular proteins
- Conformational properties and elastic behavior of protein-like lattice polymers
- Reduced protein models and their application to the protein folding problem.
- Correction to the article “Study of the Villin Headpiece folding dynamics by combining coarse‐grained Monte Carlo evolution and all‐atom molecular dynamics”
- Improved modeling of side‐chains in proteins with rotamer‐based methods: A flexible rotamer model
- Hierarchical energy-based approach to protein-structure prediction: Blind-test evaluation with CASP3 targets
- Protein folding in the post‐genomic era
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