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- M Eigen, P Schuster
- Die Naturwissenschaften
- 1977

- P Schuster, W Fontana, P F Stadler, I L Hofacker
- Proceedings. Biological sciences
- 1994

RNA folding is viewed here as a map assigning secondary structures to sequences. At fixed chain length the number of sequences far exceeds the number of structures. Frequencies of structures are highly non-uniform and follow a generalized form of Zipf's law: we find relatively few common and many rare ones. By using an algorithm for inverse folding, we show… (More)

- W Fontana, P Schuster
- Science
- 1998

To distinguish continuous from discontinuous evolutionary change, a relation of nearness between phenotypes is needed. Such a relation is based on the probability of one phenotype being accessible from another through changes in the genotype. This nearness relation is exemplified by calculating the shape neighborhood of a transfer RNA secondary structure… (More)

- S Wuchty, W Fontana, I L Hofacker, P Schuster
- Biopolymers
- 1999

An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm is particularly fast in the vicinity of the minimum free energy. This enables the efficient approximation of statistical quantities, such as the partition function or measures for structural… (More)

- C Flamm, W Fontana, I L Hofacker, P Schuster
- RNA
- 2000

We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss folding mechanisms and the correlation between the barrier structure of the conformational landscape and the folding kinetics for a number of examples based on… (More)

- W Fontana, D A Konings, P F Stadler, P Schuster
- Biopolymers
- 1993

A statistical reference for RNA secondary structures with minimum free energies is computed by folding large ensembles of random RNA sequences. Four nucleotide alphabets are used: two binary alphabets, AU and GC, the biophysical AUGC and the synthetic GCXK alphabet. RNA secondary structures are made of structural elements, such as stacks, loops, joints, and… (More)

- M Nowak, P Schuster
- Journal of theoretical biology
- 1989

The occurrence of thresholds for error propagation in asexually replicating populations is investigated by means of a simple birth and death model as well as by numerical simulation. Previous results derived for infinite population sizes are extended to finite populations. Here, replication has to be more accurate than in infinitely large populations… (More)

- Ivo L. Hofacker, Peter Schuster, Peter F. Stadler
- Discrete Applied Mathematics
- 1998

SFI Working Papers contain accounts of scientific work of the author(s) and do not necessarily represent the views of the Santa Fe Institute. We accept papers intended for publication in peer-reviewed journals or proceedings volumes, but not papers that have already appeared in print. Except for papers by our external faculty, papers must be based on work… (More)

- C Reidys, P F Stadler, P Schuster
- Bulletin of mathematical biology
- 1997

Random graph theory is used to model and analyse the relationships between sequences and secondary structures of RNA molecules, which are understood as mappings from sequence space into shape space. These maps are non-invertible since there are always many orders of magnitude more sequences than structures. Sequences folding into identical structures form… (More)

- J Swetina, P Schuster
- Biophysical chemistry
- 1982

A model for polynucleotide replication is presented and analyzed by means of perturbation theory. Two basic assumptions allow handling of sequences up to a chain length of v approximately 80 explicitly: point mutations are restricted to a two-digit model and individual sequences are subsumed into mutant classes. Perturbation theory is in excellent agreement… (More)