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MOTIVATION
Most secondary structure prediction programs target only alpha helix and beta sheet structures and summarize all other structures in the random coil pseudo class. However, such an assignment often ignores existing local ordering in so-called random coil regions. Signatures for such ordering are distinct dihedral angle pattern. For this reason, we… (More)

Thermodynamics of helix-coil transitions in amino-acid homo-oligomers are studied by the recently proposed multicanonical algorithms. Homo-oligomers of length 10 are considered for three characteristic amino acids, alanine (helix former), valine (helix indifferent), and glycine (helix breaker). For alanine other lengths (15 and 20) are also considered in… (More)

We compare a few variants of the recently proposed multicanonical method with the well known simulated annealing for the eeectiveness in search of the energy global minimum of a biomolecular system. For this we study in detail Met-enkephalin, one of the simplest peptides. We show that the new method not only outperforms simulated anneal-ing in the search of… (More)

We present a novel Monte Carlo algorithm which enhances equilibrization of low-temperature simulations and allows sampling of configurations over a large range of energies. The method is based on a non-Boltzmann probability weight factor and is another version of the so-called generalized-ensemble techniques. The effectiveness of the new approach is… (More)

We report on multicanonical simulations of the helix-coil transition of a polypeptide. The nature of this transition was studied by calculating partition function zeros and the finite size scaling of various quantities. New estimates for critical exponents are presented.

- F Fink, St Ederer, W Gronwald, Ulrich H E Hansmann, Jan H Meinke, Sandipan Mohanty +5 others
- 2008

Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise requires prior specific permission by the publisher mentioned above.… (More)

- Ulrich H E Hansmann, Luc T Wille
- 2002

We introduce a novel heuristic global optimization method, energy landscape paving (ELP), which combines core ideas from energy surface deformation and tabu search. In appropriate limits, ELP reduces to existing techniques. The approach is very general and flexible and is illustrated here on two protein folding problems. For these examples, the technique… (More)

We compare numerically the effectiveness of three recently proposed algorithms, mul-ticanonical simulations, simulations in a 1/k-ensemble, and simulated tempering, for the protein folding problem. For this we perform simulations with high statistics for one of the simplest peptides, Met-enkephalin. While the performances of all three approaches is much… (More)

We apply a recently developed method, multicanonical algorithm, to the problem of tertiary structure prediction of peptides and proteins. As a simple example to test the effectiveness of the algorithm, Met-enkephalin is studied and the ergodicity problem, or multiple-minima problem, is shown to be overcome by this algorithm. The lowest-energy conformation… (More)

We describe a revised and updated version of the program package SMMP (Simple Molecular Mechanics for Proteins) [ SMMP is an open-source FORTRAN package for molecular simulation of proteins within the standard geometry model. It is designed as a simple and inexpensive tool for researchers and students to become familiar with protein simulation techniques.… (More)