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- P Clote
- 2007

- Fabrizio Ferrè, Peter Clote
- Nucleic Acids Research
- 2005

Correctly predicting the disulfide bond topology in a protein is of crucial importance for the understanding of protein function and can be of great help for tertiary prediction methods. The web server http://clavius.bc.edu/~clotelab/DiANNA/ outputs the disulfide connectivity prediction given input of a protein sequence. The following procedure is… (More)

- Fabrizio Ferrè, Peter Clote
- Bioinformatics
- 2005

MOTIVATION
We describe a stand-alone algorithm to predict disulfide bond partners in a protein given only the amino acid sequence, using a novel neural network architecture (the diresidue neural network), and given input of symmetric flanking regions of N-terminus and C-terminus half-cystines augmented with residue secondary structure (helix, coil, sheet)… (More)

- Peter Clote
- Theor. Comput. Sci.
- 1986

- William A. Lorenz, Peter Clote
- PloS one
- 2011

An RNA secondary structure is locally optimal if there is no lower energy structure that can be obtained by the addition or removal of a single base pair, where energy is defined according to the widely accepted Turner nearest neighbor model. Locally optimal structures form kinetic traps, since any evolution away from a locally optimal structure must… (More)

- Ivan Dotu, William A. Lorenz, Pascal Van Hentenryck, Peter Clote
- Nucleic acids research
- 2010

Given an RNA sequence and two designated secondary structures A, B, we describe a new algorithm that computes a nearly optimal folding pathway from A to B. The algorithm, RNAtabupath, employs a tabu semi-greedy heuristic, known to be an effective search strategy in combinatorial optimization. Folding pathways, sometimes called routes or trajectories, are… (More)

We present results of computer experiments that indicate that several RNAs for which the native state (minimum free energy secondary structure) is functionally important (type III hammerhead ribozymes, signal recognition particle RNAs, U2 small nucleolar spliceosomal RNAs, certain riboswitches, etc.) all have lower folding energy than random RNAs of the… (More)

- Peter Clote
- Journal of Computational Biology
- 2005

We make a novel contribution to the theory of biopolymer folding, by developing an efficient algorithm to compute the number of locally optimal secondary structures of an RNA molecule, with respect to the Nussinov-Jacobson energy model. Additionally, we apply our algorithm to analyze the folding landscape of selenocysteine insertion sequence (SECIS)… (More)

- Fabrizio Ferrè, Peter Clote
- Nucleic Acids Research
- 2006

DiANNA is a recent state-of-the-art artificial neural network and web server, which determines the cysteine oxidation state and disulfide connectivity of a protein, given only its amino acid sequence. Version 1.0 of DiANNA uses a feed-forward neural network to determine which cysteines are involved in a disulfide bond, and employs a novel architecture… (More)

- Iván Dotú, Manuel Cebrián, Pascal Van Hentenryck, Peter Clote
- IEEE/ACM Transactions on Computational Biology…
- 2011

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