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- U H Hansmann, Y Okamoto
- Current opinion in structural biology
- 1999

Over the past three decades, a number of powerful simulation algorithms have been introduced to the protein folding problem. For many years, the emphasis has been placed on how to both overcome the multiple minima problem and find the conformation with the global minimum potential energy. Since the new view of the protein folding mechanism (based on the… (More)

A Fortran package is presented which provides useful routines for molecular simulation of proteins within the standard geometry model. Highly efficient algorithms for the calculation of energy and its derivatives are implemented. A set of energy minimization routines and modern Monte Carlo algorithms are added. Three different parameter sets are used to… (More)

- Ulrich H. E. Hansmann, Yuko Okamoto
- Journal of Computational Chemistry
- 1993

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)

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)

- Ulrich H. E. Hansmann, Yuko Okamoto
- Journal of Computational Chemistry
- 1997

We compare numerically the effectiveness of three recently proposed algorithms, multicanonical 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)

- Olav Zimmermann, Ulrich H. E. Hansmann
- Journal of Chemical Information and Modeling
- 2008

Constraint generation for 3d structure prediction and structure-based database searches benefit from fine-grained prediction of local structure. In this work, we present LOCUSTRA, a novel scheme for the multiclass prediction of local structure that uses two layers of support vector machines (SVM). Using a 16-letter structural alphabet from de Brevern et al.… (More)

- Frank Eisenmenger, Ulrich H. E. Hansmann, Shura Hayryan, Chin-Kun Hu
- Computer Physics Communications
- 2006

We describe a revised and updated version of the program package SMMP (Simple Molecular Mechanics for Proteins) [F. Eisenmenger, U.H.E. Hansmann, Sh. Hayryan, C.-K. Hu, Comput. Phys. Comm. 138 (2001) 192–212]. SMMP is an open-source FORTRAN package for molecular simulation of proteins within the standard geometry model. It is designed as a simple and… (More)

Themulticanonical ansatz is used to study variations in the energy landscape of a small peptide, Met-enkephalin, under a change from the ECEPP/2 force field to ECEPP/3. Local minima with energies up to 5 kcal/mol higher than the global minima are sampled and classified according to H-bridges and backbone angles. The distribution and relative weight for… (More)

The effectiveness of a new algorithm, parallel tempering, is studied for numerical simulations of biological molecules. These molecules suffer from a rough energy landscape. The resulting slowing down in numerical simulations is overcome by the new method. This is demonstrated by performing simulations with high statistics for one of the simplest peptides,… (More)

- Ulrich H E Hansmann, Luc T Wille
- Physical review letters
- 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)