@article {2016|1711,
	title = {In silico structural characterization of protein targets for drug development against Trypanosoma cruzi},
	journal = {J. Mol. Model.},
	volume = {22},
	number = {10},
	year = {2016},
	month = {oct},
	abstract = {Trypanosoma cruzi is the protozoan pathogen responsible for Chagas disease, which is a major public health problem in tropical and subtropical regions of developing countries and particularly in Brazil. Despite many studies, there is no efficient treatment against Chagas disease, and the search for new therapeutic targets specific to T. cruzi is critical for drug development. Here, we have revisited 41 protein sequences proposed by the analogous enzyme pipeline, and found that it is possible to provide structures for T. cruzi sequences with clear homologs or analogs in H. sapiens and likely associated with trypanothione reductase, cysteine synthase, and ATPase functions, and structures for sequences specific to T. cruzi and absent in H. sapiens associated with 2,4-dienoyl-CoA reductase, and leishmanolysin activities. The implications of our structures refined by atomistic molecular dynamics (monomer or dimer states) in their in vitro environments (aqueous solution or membrane bilayers) are discussed for drug development and suggest that all protein targets, except cysteine synthase, merit further investigation.},
	issn = {1610-2940},
	doi = {10.1007/s00894-016-3115-9},
	author = {Lima, Carlyle Ribeiro and Carels, Nicolas and Ramos Guimaraes, Ana Carolina and Pierre Tuffery and Philippe Derreumaux}
}
@article {2016|1733,
	title = {PEP-FOLD3: faster denovo structure prediction for linear peptides in solution and in complex},
	journal = {Nucleic Acids Res.},
	volume = {44},
	number = {W1},
	year = {2016},
	pages = {W449-W454},
	abstract = {Structure determination of linear peptides of 5-50 amino acids in aqueous solution and interacting with proteins is a key aspect in structural biology. PEP-FOLD3 is a novel computational framework, that allows both (i) de novo free or biased prediction for linear peptides between 5 and 50 amino acids, and (ii) the generation of native-like conformations of peptides interacting with a protein when the interaction site is known in advance. PEP-FOLD3 is fast, and usually returns solutions in a few minutes. Testing PEP-FOLD3 on 56 peptides in aqueous solution led to experimental-like conformations for 80\% of the targets. Using a benchmark of 61 peptide-protein targets starting from the unbound form of the protein receptor, PEP-FOLD3 was able to generate peptide poses deviating on average by 3.3 angstrom from the experimental conformation and return a native-like pose in the first 10 clusters for 52\% of the targets. PEP-FOLD3 is available at http://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3.},
	issn = {0305-1048},
	doi = {10.1093/nar/gkw329},
	author = {Lamiable, Alexis and Thevenet, Pierre and Rey, Julien and Vavrusa, Marek and Philippe Derreumaux and Pierre Tuffery}
}
@article {2014|1893,
	title = {Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction},
	journal = {J. Chem. Theory Comput.},
	volume = {10},
	number = {10},
	year = {2014},
	month = {oct},
	pages = {4745{\textendash}4758},
	doi = {10.1021/ct500592m},
	author = {Shen, Yimin and Maupetit, Julien and Philippe Derreumaux and Pierre Tuffery}
}
@article {2014|1798,
	title = {The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems},
	journal = {Chem. Soc. Rev.},
	volume = {43},
	number = {13},
	year = {2014},
	pages = {4871{\textendash}4893},
	doi = {10.1039/c4cs00048j},
	author = {F. Sterpone and S. Melchionna and Pierre Tuffery and S. Pasquali and N. Mousseau and T. Cragnolini and Y Chebaro and J.-F. St-Pierre and M. Kalimeri and A. Barducci and Y. Laurin and A. Tek and Marc Baaden and Phuong Hoang Nguyen and Philippe Derreumaux}
}
@article {2012|1911,
	title = {Delivering the native structures of peptides from computer simulations and predicted NMR proton chemical shifts},
	journal = {J. Pept. Sci.},
	volume = {18},
	number = {1},
	year = {2012},
	month = {sep},
	pages = {S38},
	author = {Thevenet, P. and Shen, Y. and Maupetit, J. and Guyon, F. and Padilla, A. and Philippe Derreumaux and Pierre Tuffery}
}
@article {2012|1932,
	title = {Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches},
	journal = {Journal of the Royal Society Interface},
	volume = {9},
	number = {66},
	year = {2012},
	month = {jan},
	pages = {20{\textendash}33},
	doi = {10.1098/rsif.2011.0584},
	author = {Pierre Tuffery and Philippe Derreumaux}
}
@article {2012|1944,
	title = {PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides},
	journal = {Nucleic Acids Res.},
	volume = {40},
	number = {W1},
	year = {2012},
	month = {jul},
	pages = {W288-W293},
	doi = {10.1093/nar/gks419},
	author = {Thevenet, Pierre and Shen, Yimin and Maupetit, Julien and Guyon, Frederic and Philippe Derreumaux and Pierre Tuffery}
}
@article {2010|1901,
	title = {A Fast Method for Large-Scale De Novo Peptide and Miniprotein Structure Prediction},
	journal = {J. Comput. Chem.},
	volume = {31},
	number = {4},
	year = {2010},
	month = {mar},
	pages = {726{\textendash}738},
	doi = {10.1002/jcc.21365},
	author = {Maupetit, Julien and Philippe Derreumaux and Pierre Tuffery}
}
@article {2009|1436,
	title = {A fast method for large-scale De Novo peptide and miniprotein structure prediction.},
	journal = {J. Comput. Chem.},
	year = {2009},
	month = {jun},
	doi = {10.1002/jcc.21365},
	author = {Julien Maupetit and Philippe Derreumaux and Pierre Tuffery}
}
@article {2009|1942,
	title = {PEP-FOLD: an online resource for de novo peptide structure prediction.},
	journal = {Nucleic Acids Res.},
	volume = {37},
	number = {Web Server issue},
	year = {2009},
	month = {jul},
	pages = {W498{\textendash}W503},
	keywords = {Algorithms, Internet, Models, Molecular, Peptides, Protein, Protein Conformation, Reproducibility of Results, Sequence Analysis, Software, User-Computer Interface},
	doi = {10.1093/nar/gkp323},
	author = {Julien Maupetit and Philippe Derreumaux and Pierre Tuffery}
}
@article {2009|1734,
	title = {PEP-FOLD: an online resource for de novo peptide structure prediction},
	journal = {Nucleic Acids Res.},
	volume = {37},
	year = {2009},
	month = {jul},
	pages = {W498-W503},
	doi = {10.1093/nar/gkp323},
	author = {Maupetit, Julien and Philippe Derreumaux and Pierre Tuffery}
}
@article {2007|1985,
	title = {A coarse-grained protein force field for folding and structure prediction},
	journal = {Proteins: Struct., Funct., Bioinf.},
	volume = {69},
	number = {2},
	year = {2007},
	month = {nov},
	pages = {394{\textendash}408},
	doi = {10.1002/prot.21505},
	author = {Maupetit, Julien and Pierre Tuffery and Philippe Derreumaux}
}
@article {2005|1979,
	title = {Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm},
	journal = {Proteins: Struct., Funct., Bioinf.},
	volume = {61},
	number = {4},
	year = {2005},
	month = {dec},
	pages = {732{\textendash}740},
	doi = {10.1002/prot.20698},
	author = {Pierre Tuffery and Philippe Derreumaux}
}
@article {2005|1900,
	title = {Improved greedy algorithm for protein structure reconstruction},
	journal = {J. Comput. Chem.},
	volume = {26},
	number = {5},
	year = {2005},
	month = {apr},
	pages = {506{\textendash}513},
	doi = {10.1002/jcc.20181},
	author = {Pierre Tuffery and Guyon, F and Philippe Derreumaux}
}
