The RCSB Protein Data Bank: new resources for research and education, Nucleic Acids Research, vol.41, issue.D1, pp.475-482, 2013. ,
DOI : 10.1093/nar/gks1200
GenBank, Nucleic Acids Research, vol.40, issue.D1, pp.48-53, 2012. ,
DOI : 10.1093/nar/gkr1202
URL : http://doi.org/10.1093/nar/gkj157
Protein Structure Prediction and Structural Genomics, Science, vol.294, issue.5540, pp.93-96, 2001. ,
DOI : 10.1126/science.1065659
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.82.1058
Comparative protein structure modeling using MODELLER, Curr. Protoc. Bioinformatics, Chapter, 2006. ,
Protein Structure Modeling with MODELLER, Methods Mol. Biol, vol.426, pp.145-159, 2008. ,
DOI : 10.1007/978-1-60327-058-8_8
On the Accuracy of Homology Modeling and Sequence Alignment Methods Applied to Membrane Proteins, Biophysical Journal, vol.91, issue.2, pp.508-517, 2006. ,
DOI : 10.1529/biophysj.106.082313
Comparative Modeling: The State of the Art and Protein Drug Target Structure Prediction, Combinatorial Chemistry & High Throughput Screening, vol.14, issue.6, pp.532-547, 2011. ,
DOI : 10.2174/138620711795767811
Template-Based Protein Structure Modeling, Methods Mol. Biol, vol.673, pp.73-94, 2010. ,
DOI : 10.1007/978-1-60761-842-3_6
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108304
Template-Based Protein Modeling: Recent Methodological Advances, Current Topics in Medicinal Chemistry, vol.10, issue.1, pp.84-94, 2010. ,
DOI : 10.2174/156802610790232314
Utility of homology models in the drug discovery process, Drug Discovery Today, vol.9, issue.15, pp.659-669, 2004. ,
DOI : 10.1016/S1359-6446(04)03196-4
All are not equal: A benchmark of different homology modeling programs, Protein Science, vol.53, issue.5, pp.1315-1327, 2005. ,
DOI : 10.1110/ps.041253405
Structure-based model of allostery predicts coupling between distant sites, Proc. Natl Acad. Sci. USA, pp.4875-4880, 2012. ,
DOI : 10.1073/pnas.1116274109
Macromolecular docking restrained by a small angle X-ray scattering profile, Journal of Structural Biology, vol.173, issue.3, pp.461-471, 2011. ,
DOI : 10.1016/j.jsb.2010.09.023
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3040266
Statistical Potential for Modeling and Ranking of Protein???Ligand Interactions, Journal of Chemical Information and Modeling, vol.51, issue.12, pp.3078-3092, 2011. ,
DOI : 10.1021/ci200377u
Tools for comparative protein structure modeling and analysis, Nucleic Acids Research, vol.31, issue.13, pp.3375-3380, 2003. ,
DOI : 10.1093/nar/gkg543
Comparative Protein Modelling by Satisfaction of Spatial Restraints, Journal of Molecular Biology, vol.234, issue.3, pp.779-815, 1993. ,
DOI : 10.1006/jmbi.1993.1626
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997. ,
DOI : 10.1093/nar/25.17.3389
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment, Nature Methods, vol.11, issue.2, pp.173-175, 2012. ,
DOI : 10.1006/jmbi.1993.1626
URL : http://hdl.handle.net/11858/00-001M-0000-0015-8D56-A
Protein homology detection by HMM-HMM comparison, Bioinformatics, vol.21, issue.7, pp.951-960, 2005. ,
DOI : 10.1093/bioinformatics/bti125
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.519.1257
Identification of common molecular subsequences, Journal of Molecular Biology, vol.147, issue.1, pp.195-197, 1981. ,
DOI : 10.1016/0022-2836(81)90087-5
Comparative protein structure modeling using Modeller, Curr. Protoc. Bioinformatics, 2006. ,
Alignment of protein sequences by their profiles, Protein Science, vol.13, issue.4, pp.1071-1087, 2004. ,
DOI : 10.1110/ps.03379804
Statistical potential for assessment and prediction of protein structures, Protein Science, vol.12, issue.11, pp.2507-2524, 2006. ,
DOI : 10.1110/ps.062416606
Fold assessment for comparative protein structure modeling, Protein Science, vol.11, issue.11, pp.2412-2426, 2007. ,
DOI : 10.1110/ps.072895107
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2211691
ModBase, a database of annotated comparative protein structure models, and associated resources, Nucleic Acids Research, vol.39, issue.Database, pp.465-474, 2011. ,
DOI : 10.1093/nar/gkq1091
URL : https://hal.archives-ouvertes.fr/pasteur-01414232
How well can the accuracy of comparative protein structure models be predicted?, Protein Science, vol.11, issue.11, pp.1881-1893, 2008. ,
DOI : 10.1110/ps.036061.108
Optimized atomic statistical potentials: Assessment of protein interfaces and loops (epub ahead of print, 2013. ,
A method for integrative structure determination of protein-protein complexes, Bioinformatics, vol.28, issue.24, pp.3282-3289, 2012. ,
DOI : 10.1093/bioinformatics/bts628
ZRANK: Reranking protein docking predictions with an optimized energy function, Proteins: Structure, Function, and Bioinformatics, vol.16, issue.4, pp.1078-1086, 2007. ,
DOI : 10.1002/prot.21373
FireDock: Fast interaction refinement in molecular docking, Proteins: Structure, Function, and Bioinformatics, vol.20, issue.1, pp.139-159, 2007. ,
DOI : 10.1002/prot.21495
A hierarchical approach to all-atom protein loop prediction, Proteins: Structure, Function, and Bioinformatics, vol.1, issue.2, pp.351-367, 2004. ,
DOI : 10.1002/prot.10613
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.115.911
Generalized Fragment Picking in Rosetta: Design, Protocols and Applications, PLoS ONE, vol.22, issue.8, p.23294, 2011. ,
DOI : 10.1371/journal.pone.0023294.s001
URL : http://doi.org/10.1371/journal.pone.0023294
Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential, Protein Science, vol.13, issue.2, pp.391-399, 2004. ,
DOI : 10.1110/ps.03411904
Finding Cures for Tropical Diseases: Is Open Source an Answer?, PLoS Medicine, vol.296, issue.3, p.56, 2004. ,
DOI : 10.1371/journal.pmed.0010056.g001
URL : http://doi.org/10.1371/journal.pmed.0010056
A Kernel for Open Source Drug Discovery in Tropical Diseases, PLoS Neglected Tropical Diseases, vol.76, issue.8132, p.418, 2009. ,
DOI : 10.1371/journal.pntd.0000418.s004
Genomic-scale prioritization of drug targets: the TDR Targets database, Nature Reviews Drug Discovery, vol.278, issue.11, pp.900-907, 2008. ,
DOI : 10.1038/nrd2684
Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis, PLoS Computational Biology, vol.30, issue.4, p.1003253, 2013. ,
DOI : 10.1371/journal.pcbi.1003253.s003
Structure of a putative BenF-like porin from Pseudomonas fluorescens Pf-5 at 2.6 ?? resolution, Proteins: Structure, Function, and Bioinformatics, vol.37, issue.Database issue, pp.3056-3062, 2010. ,
DOI : 10.1002/prot.22829
Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies, Journal of Structural and Functional Genomics, vol.25, issue.2, pp.107-125, 2009. ,
DOI : 10.1007/s10969-008-9056-5
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources, Bioinformatics, vol.21, issue.12, pp.2814-2820, 2005. ,
DOI : 10.1093/bioinformatics/bti442
ModLoop: automated modeling of loops in protein structures, Bioinformatics, vol.19, issue.18, pp.2500-2501, 2003. ,
DOI : 10.1093/bioinformatics/btg362
PIBASE: a comprehensive database of structurally defined protein interfaces, Bioinformatics, vol.21, issue.9, pp.1901-1907, 2005. ,
DOI : 10.1093/bioinformatics/bti277
DBAli tools: mining the protein structure space, Nucleic Acids Research, vol.35, issue.Web Server, pp.393-397, 2007. ,
DOI : 10.1093/nar/gkm236
DBAli: a database of protein structure alignments, Bioinformatics, vol.17, issue.8, pp.746-747, 2001. ,
DOI : 10.1093/bioinformatics/17.8.746
MODBASE, a database of annotated comparative protein structure models and associated resources, Nucleic Acids Research, vol.37, issue.Database, pp.347-354, 2009. ,
DOI : 10.1093/nar/gkn791
URL : https://hal.archives-ouvertes.fr/pasteur-01414232
MODBASE: a database of annotated comparative protein structure models and associated resources, Nucleic Acids Research, vol.34, issue.90001, pp.291-295, 2006. ,
DOI : 10.1093/nar/gkj059
URL : https://hal.archives-ouvertes.fr/pasteur-01414232
SALIGN: a web server for alignment of multiple protein sequences and structures, Bioinformatics, vol.28, issue.15, pp.2072-2073, 2012. ,
DOI : 10.1093/bioinformatics/bts302
Database issue 51 FoXS: a web server for rapid computation and fitting of SAXS Profiles, D344 Nucleic Acids Research, pp.541-544, 2010. ,
Studies on protein folding, unfolding, and fluctuations by computer simulation. II. A. Three-dimensional lattice model of lysozyme, Biopolymers, vol.8, issue.6, pp.1531-1548, 1978. ,
DOI : 10.1002/bip.1978.360170612
Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations, Proc. Natl Acad. Sci. USA, pp.11844-11849, 2006. ,
DOI : 10.1073/pnas.0604375103
An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields, Proteins: Structure, Function, and Bioinformatics, vol.18, issue.2, pp.430-441, 2009. ,
DOI : 10.1002/prot.22253
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439813
Impact of Mutations on the Allosteric Conformational Equilibrium, Journal of Molecular Biology, vol.425, issue.3, pp.647-661, 2013. ,
DOI : 10.1016/j.jmb.2012.11.041
Analysis of X-ray and neutron scattering from biomacromolecular solutions, Current Opinion in Structural Biology, vol.17, issue.5, pp.562-571, 2007. ,
DOI : 10.1016/j.sbi.2007.06.009
Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS), Nature Methods, vol.334, issue.8, pp.606-612, 2009. ,
DOI : 10.3109/00365515309094189
??? a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates, Journal of Applied Crystallography, vol.28, issue.6, pp.768-773, 1995. ,
DOI : 10.1107/S0021889895007047
AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models, Nucleic Acids Research, vol.39, issue.suppl, pp.184-189, 2011. ,
DOI : 10.1093/nar/gkr430
URL : https://hal.archives-ouvertes.fr/cea-00666216
Computation of small-angle scattering profiles with three-dimensional Zernike polynomials, Acta Crystallographica Section A Foundations of Crystallography, vol.377, issue.2, pp.278-285, 2012. ,
DOI : 10.1107/S010876731104788X
: A unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes, The Journal of Chemical Physics, vol.138, issue.2, p.24112, 2013. ,
DOI : 10.1063/1.4774148
Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments, Biophysical Journal, vol.105, issue.4, pp.962-974, 2013. ,
DOI : 10.1016/j.bpj.2013.07.020
URL : http://doi.org/10.1016/j.bpj.2013.07.020
XRCC4 Protein Interactions with XRCC4-like Factor (XLF) Create an Extended Grooved Scaffold for DNA Ligation and Double Strand Break Repair, Journal of Biological Chemistry, vol.286, issue.37, pp.32638-32650, 2011. ,
DOI : 10.1074/jbc.M111.272641
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3173232
Structure and flexibility within proteins as identified through small angle X-ray scattering, General Physiology and Biophysics, vol.28, issue.2, pp.174-189, 2009. ,
DOI : 10.4149/gpb_2009_02_174
Small angle X-ray scattering as a complementary tool for high-throughput structural studies, Biopolymers, vol.129, issue.8, pp.517-530, 2011. ,
DOI : 10.1002/bip.21630
: a Windows PC-based system for small-angle scattering data analysis, Journal of Applied Crystallography, vol.36, issue.5, pp.1277-1282, 2003. ,
DOI : 10.1107/S0021889803012779
Protein docking and complementarity, Journal of Molecular Biology, vol.221, issue.1, pp.327-346, 1991. ,
DOI : 10.1016/0022-2836(91)80222-G
Coordinating the impact of structural genomics on the human ??-helical transmembrane proteome, Nature Structural & Molecular Biology, vol.19, issue.2, pp.135-138, 2013. ,
DOI : 10.1093/nar/gkn201
NCBI BLAST: a better web interface, Nucleic Acids Research, vol.36, issue.Web Server, pp.5-9, 2008. ,
DOI : 10.1093/nar/gkn201
The DISOPRED server for the prediction of protein disorder, Bioinformatics, vol.20, issue.13, pp.2138-2139, 2004. ,
DOI : 10.1093/bioinformatics/bth195
IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content, Bioinformatics, vol.21, issue.16, pp.3433-3434, 2005. ,
DOI : 10.1093/bioinformatics/bti541
Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology, The EMBO Journal, vol.57, issue.10, pp.1478-1488, 2013. ,
DOI : 10.1016/j.cell.2010.04.012
Scanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks, Glycobiology, vol.9, issue.10, pp.1009-1022, 1999. ,
DOI : 10.1093/glycob/9.10.1009
PSI:Biology-materials repository: a biologist???s resource for protein expression plasmids, Journal of Structural and Functional Genomics, vol.77, issue.11, pp.55-62, 2011. ,
DOI : 10.1007/s10969-011-9100-8
hORFeome v3.1: A resource of human open reading frames representing over 10,000 human genes, Genomics, vol.89, issue.3, pp.307-315, 2007. ,
DOI : 10.1016/j.ygeno.2006.11.012
The completion of the mammalian gene collection, 2009. ,
genenames.org: the HGNC resources in 2011, Nucleic Acids Research, vol.39, issue.Database, pp.514-519, 2011. ,
DOI : 10.1093/nar/gkq892
The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource, Journal of Structural and Functional Genomics, vol.12, issue.2, pp.57-62, 2012. ,
DOI : 10.1007/s10969-012-9133-7
HIV-1 replication, Somatic Cell and Molecular Genetics, vol.26, issue.1/6, pp.13-33, 2001. ,
DOI : 10.1023/A:1021070512287
Human Immunodeficiency Virus Type 1 Protease Inhibitors, Archives of Internal Medicine, vol.157, issue.9, pp.951-959, 1997. ,
DOI : 10.1001/archinte.1997.00440300037003
Emerging principles in protease-based drug discovery, Nature Reviews Drug Discovery, vol.23, issue.9, pp.690-701, 2010. ,
DOI : 10.1038/nrd3053
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2974563
HIV-protease inhibitors, N. Engl. J. Med, vol.338, pp.1281-1292, 1998. ,
Active human immunodeficiency virus protease is required for viral infectivity., Proc. Natl Acad. Sci. USA, pp.4686-4690, 1988. ,
DOI : 10.1073/pnas.85.13.4686
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC280500
The crystal structures at 2.2-A resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations, J. Biol. Chem, vol.267, pp.22770-22778, 1992. ,
How does a symmetric dimer recognize an asymmetric substrate? a substrate complex of HIV-1 protease, Journal of Molecular Biology, vol.301, issue.5, pp.1207-1220, 2000. ,
DOI : 10.1006/jmbi.2000.4018
Structural implications of drug-resistant mutants of HIV-1 protease: High-resolution crystal structures of the mutant protease/substrate analogue complexes, Proteins: Structure, Function, and Genetics, vol.32, issue.4, pp.455-464, 2001. ,
DOI : 10.1002/prot.1057
Analysis of HIV protease killing through caspase 8 reveals a novel interaction between caspase 8 and mitochondria, Open Virol. J, vol.1, pp.39-46, 2007. ,
HIV protease cleavage of procaspase 8 is necessary for death of HIVinfected cells, Open Virol. J, vol.2, pp.1-7, 2008. ,
HIV- 1 Protease Inhibits Cap- and Poly(A)-Dependent Translation upon eIF4GI and PABP Cleavage, PLoS ONE, vol.4, issue.11, p.7997, 2009. ,
DOI : 10.1371/journal.pone.0007997.s002
A catalogue of putative HIV-1 protease host cell substrates, Biological Chemistry, vol.393, issue.9, pp.915-931, 2012. ,
DOI : 10.1515/hsz-2012-0168
Structural Analysis Reveals Conformational Plasticity in the Recognition of RNA 3??? Ends by the Human La Protein, Structure, vol.16, issue.6, pp.852-862, 2008. ,
DOI : 10.1016/j.str.2008.02.021
Cluster analysis of amino acid indices for prediction of protein structure and function, "Protein Engineering, Design and Selection", vol.2, issue.2, pp.93-100, 1988. ,
DOI : 10.1093/protein/2.2.93
Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins, "Protein Engineering, Design and Selection", vol.9, issue.1, pp.27-36, 1996. ,
DOI : 10.1093/protein/9.1.27
Protein secondary structure prediction based on position-specific scoring matrices, Journal of Molecular Biology, vol.292, issue.2, pp.195-202, 1999. ,
DOI : 10.1006/jmbi.1999.3091
Random forests, Machine Learning, vol.45, issue.1, pp.5-32, 2001. ,
DOI : 10.1023/A:1010933404324
GenBank, Nucleic Acids Research, vol.38, issue.Database, pp.46-51, 2010. ,
DOI : 10.1093/nar/gkp1024
URL : http://doi.org/10.1093/nar/gkj157
MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures, Journal of Applied Crystallography, vol.24, issue.5, pp.946-950, 1991. ,
DOI : 10.1107/S0021889891004399
[26] Raster3D: Photorealistic molecular graphics, Methods Enzymol, vol.277, pp.505-524, 1997. ,
DOI : 10.1016/S0076-6879(97)77028-9
UCSF Chimera?A visualization system for exploratory research and analysis, Journal of Computational Chemistry, vol.373, issue.13, pp.1605-1612, 2004. ,
DOI : 10.1002/jcc.20084
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.456.9442
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure Remediation of the protein data bank archive, PLoS Comp. Biol. Nucleic Acids Res, vol.5, issue.36, pp.426-433, 2008. ,
The Universal Protein Resource (UniProt): an expanding universe of protein information, Nucleic Acids Research, vol.34, issue.90001, pp.187-191, 2006. ,
DOI : 10.1093/nar/gkj161
The UCSC Genome Browser database: update 2010, Nucleic Acids Research, vol.38, issue.Database, pp.613-619, 2010. ,
DOI : 10.1093/nar/gkp939
URL : http://doi.org/10.1093/nar/gkp939
InterPro: the integrative protein signature database, Nucleic Acids Research, vol.37, issue.Database, pp.211-215, 2009. ,
DOI : 10.1093/nar/gkn785
URL : https://hal.archives-ouvertes.fr/hal-00428250
Integrating genotype and phenotype information: an overview of the PharmGKB project, The Pharmacogenomics Journal, vol.16, issue.3, pp.167-170, 2001. ,
DOI : 10.1038/sj.tpj.6500035
The Protein Model Portal--a comprehensive resource for protein structure and model information, Database, vol.2013, issue.0, p.31, 2013. ,
DOI : 10.1093/database/bat031
Outcome of a Workshop on Applications of Protein Models in Biomedical Research, Structure, vol.17, issue.2, pp.151-159, 2009. ,
DOI : 10.1016/j.str.2008.12.014
The Universal Protein Resource (UniProt), Nucleic Acids Research, vol.33, issue.Database issue, pp.154-159, 2005. ,
DOI : 10.1093/nar/gki070
URL : http://doi.org/10.1093/nar/gki070
New year, new PubMed. Eur, J. Phys. Rehabil. Med, vol.45, pp.155-159, 2009. ,