Biomedical subjects

Pierre Tufféry

Publications and source records attributed to Pierre Tufféry.

4 recordsLinked to original sources

PubMed2006

SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace.

SABBAC is an on-line service devoted to protein backbone reconstruction from alpha-carbon trace. It is based on the assembly of fragments taken from a library of reduced size, selected from the encoding of the protein trace in a hidden Markov model-derived structural alphabet. The assembly of the fragments is achieved by a greedy algorithm, using an energy-based scoring. Alpha-carbon coordinates remain unaffected. SABBAC simply positions the missing backbone atoms, no further refinement is performed. From our tests, SABBAC performs equal or better than other similar on-line approach and is robust to deviations on the alpha-carbon coordinates. It can be accessed at http://bioserv.rpbs.jussieu.fr/SABBAC.html.

Carbon↗

PubMed2005

PCE: web tools to compute protein continuum electrostatics.

PCE (protein continuum electrostatics) is an online service for protein electrostatic computations presently based on the MEAD (macroscopic electrostatics with atomic detail) package initially developed by D. Bashford [(2004) Front Biosci., 9, 1082-1099]. This computer method uses a macroscopic electrostatic model for the calculation of protein electrostatic properties, such as pK(a) values of titratable groups and electrostatic potentials. The MEAD package generates electrostatic energies via finite difference solution to the Poisson-Boltzmann equation. Users submit a PDB file and PCE returns potentials and pK(a) values as well as color (static or animated) figures displaying electrostatic potentials mapped on the molecular surface. This service is intended to facilitate electrostatics analyses of proteins and thereby broaden the accessibility to continuum electrostatics to the biological community. PCE can be accessed at http://bioserv.rpbs.jussieu.fr/PCE.

Hydrogen-Ion Concentration↗

PubMed2005

PPG: online generation of protein pictures and animations.

The protein picture generator (PPG) is an online service to generate pictures of a protein structure. Its design was conceived as an answer to the need expressed by a part of the community to have some means to produce simply complex pictures to insert in publications or in presentations. PPG can produce static or animated pictures. It can be accessed at http://bioserv.rpbs.jussieu.fr/cgi-bin/PPG.

Computer Graphics↗

PubMed2004

SA-Search: a web tool for protein structure mining based on a Structural Alphabet.

SA-Search is a web tool that can be used to mine for protein structures and extract structural similarities. It is based on a hidden Markov model derived Structural Alphabet (SA) that allows the compression of three-dimensional (3D) protein conformations into a one-dimensional (1D) representation using a limited number of prototype conformations. Using such a representation, classical methods developed for amino acid sequences can be employed. Currently, SA-Search permits the performance of fast 3D similarity searches such as the extraction of exact words using a suffix tree approach, and the search for fuzzy words viewed as a simple 1D sequence alignment problem. SA-Search is available at http://bioserv.rpbs.jussieu.fr/cgi-bin/SA-Search.

Amino Acid Sequence↗