Journal Article10.1021/JP991014Y
An Efficient Deformation-Based Global Optimization Method for Off-Lattice Polymer Chains: Self-Consistent Basin-to-Deformed-Basin Mapping (SCBDBM). Application to United-Residue Polypeptide Chains
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TL;DR: A new method to surmount the multiple-minima problem in protein folding is proposed to locate a group of large basins containing low-energy minima.
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Abstract: A new method to surmount the multiple-minima problem in protein folding is proposed. Its underlying principle is to locate a group of large basins containing low-energy minima (hereafter referred t...
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Citations
Global optimization of clusters, crystals, and biomolecules
TL;DR: Some recent progress in finding the global minima of potential energy functions is described, focusing on applications of the simple "basin-hopping" approach to atomic and molecular clusters and more complicated hypersurface deformation techniques for crystals and biomolecules.
Long-timescale simulation methods
TL;DR: It is not difficult to find molecular processes in biology that span more than ten orders of magnitude of relevant times, making the straightforward simulation of these events very difficult.
177
Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding.
TL;DR: A novel Monte Carlo algorithm called parallel hyperbolic sampling (PHS) is developed that logarithmically flattens local high‐energy barriers and, therefore, allows the simulation to tunnel more efficiently through energetically inaccessible regions to low‐energy valleys.
Replica Exchange and Multicanonical Algorithms with the Coarse-Grained United-Residue (UNRES) Force Field
TL;DR: Calculated thermodynamic averages, such as canonical average energy and heat capacity, are in good agreement among all simulations for poly-L-alanine, showing that the algorithms were implemented correctly, and that all three algorithms are equally effective for small systems.
References
On finding transition states
TL;DR: In this paper, an algorithm for locating transition states on a potential energy surface is described, which makes explicit use of the second derivative matrix of the potential surface, is able to "walk uphill" from the minimum on a possible surface to the transition state essentially automatically.
United-residue force field for off-lattice protein-structure simulations: III. Origin of backbone hydrogen-bonding cooperativity in united-residue potentials
Adam Liwo,Adam Liwo,Adam Liwo,R. Kazmierkiewicz,Cezary Czaplewski,Małgorzata Groth,Stanisław Ołdziej,Ryszard J. Wawak,S. Rackovsky,Matthew R. Pincus,Harold A. Scheraga +10 more
TL;DR: Based on the dipole model of peptide groups developed in this paper, a cumulant expansion of the average free energy of the system of freely rotating peptide-group dipoles tethered to a fixed α-carbon trace is derived.
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Global energy minimum searches using an approximate solution of the imaginary time Schroedinger equation
TL;DR: In this article, a method for finding the global energy minimum of a multidimensional potential energy surface through an approximate solution of the Schrodinger equation in imaginary time is presented.
140
Application of the diffusion equation method for global optimization to oligopeptides
TL;DR: In this article, the diffusion equation is modified for a conformational analysis of two peptides, terminally-blocked alanine and the pentapeptide Met-enkephalin.
136
De novo and inverse folding predictions of protein structure and dynamics
TL;DR: A very high coordination number lattice model that can predict the 3D structure of a number of globular proteins de novo using just the amino acid sequence is described, and this inverse folding algorithm is generalized to predict elements of supersecondary structure including β-hairpins, helical hairpins and α/β/α fragments.
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