PepComposer: computational design of peptides binding to a given protein surface
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Anna Tramontano | Rosalba Lepore | Alfredo Iacoangeli | Agnieszka Obarska-Kosinska | A. Tramontano | R. Lepore | A. Iacoangeli | A. Obarska-Kosinska | A. Obarska-Kosińska
[1] François Stricher,et al. PepX: a structural database of non-redundant protein–peptide complexes , 2009, Nucleic Acids Res..
[2] Sergey Lyskov,et al. PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta , 2010, Bioinform..
[3] Jiong Yang,et al. CLUSEQ: efficient and effective sequence clustering , 2003, Proceedings 19th International Conference on Data Engineering (Cat. No.03CH37405).
[4] Gregory A Caputo,et al. Supporting Online Material for Computational Design of Peptides That Target Transmembrane Helices , 2007 .
[5] P. Bradley,et al. Toward High-Resolution de Novo Structure Prediction for Small Proteins , 2005, Science.
[6] J. Anglister,et al. Peptides in the treatment of AIDS. , 2009, Current opinion in structural biology.
[7] Nir London,et al. The structural basis of peptide-protein binding strategies. , 2010, Structure.
[8] Christopher L. McClendon,et al. Reaching for high-hanging fruit in drug discovery at protein–protein interfaces , 2007, Nature.
[9] Anna Tramontano,et al. Cancer-Selective Targeting of the NF-κB Survival Pathway with GADD45β/MKK7 Inhibitors , 2014, Cancer cell.
[10] L. Serrano,et al. Protein-peptide interactions adopt the same structural motifs as monomeric protein folds. , 2009, Structure.
[11] Philip Bradley,et al. Structure‐based prediction of protein–peptide specificity in rosetta , 2010, Proteins.
[12] Aric Hagberg,et al. Exploring Network Structure, Dynamics, and Function using NetworkX , 2008, Proceedings of the Python in Science Conference.
[13] Jack Snoeyink,et al. Scientific benchmarks for guiding macromolecular energy function improvement. , 2013, Methods in enzymology.
[14] H. Nar,et al. Ligand bioactive conformation plays a critical role in the design of drugs that target the hepatitis C virus NS3 protease. , 2014, Journal of medicinal chemistry.
[15] Björn Windshügel,et al. LEADS-PEP: A Benchmark Data Set for Assessment of Peptide Docking Performance , 2016, J. Chem. Inf. Model..
[16] Haim J. Wolfson,et al. Geometric hashing: an overview , 1997 .
[17] Emiko Fire,et al. The MCL-1 BH3 Helix is an Exclusive MCL-1 inhibitor and Apoptosis Sensitizer , 2010, Nature chemical biology.
[18] R. Bartenschlager,et al. Determinants of substrate specificity in the NS3 serine proteinase of the hepatitis C virus. , 1997, Virology.
[19] Leszek Gasieniec,et al. Proceedings of the eighteenth annual ACM-SIAM symposium on discrete algorithms , 2007, SODA 2007.
[20] Dan L. Sackett,et al. Protein-protein interactions: making drug design second nature. , 2009, Nature chemistry.
[21] Gevorg Grigoryan,et al. Design of protein-interaction specificity affords selective bZIP-binding peptides , 2009, Nature.
[22] M. Murcko,et al. Crystal Structure of the Hepatitis C Virus NS3 Protease Domain Complexed with a Synthetic NS4A Cofactor Peptide , 1996, Cell.
[23] Burak Erman,et al. VitAL: Viterbi Algorithm for de novo Peptide Design , 2010, PloS one.
[24] Joost Schymkowitz,et al. Computational design of peptide ligands. , 2011, Trends in biotechnology.
[25] Jens Meiler,et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. , 2011, Methods in enzymology.
[26] Ming Zhang,et al. Comparing sequences without using alignments: application to HIV/SIV subtyping , 2007, BMC Bioinformatics.
[27] H. Wolfson,et al. Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. , 1991, Proceedings of the National Academy of Sciences of the United States of America.
[28] Raymond E. Moellering,et al. Direct inhibition of the NOTCH transcription factor complex , 2010, Nature.
[29] Nir London,et al. Rosetta FlexPepDock ab-initio: Simultaneous Folding, Docking and Refinement of Peptides onto Their Receptors , 2011, PloS one.
[30] Stefan Wallin,et al. Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening , 2013, PLoS Comput. Biol..
[31] D. Lamarre,et al. Peptide-based inhibitors of the hepatitis C virus serine protease. , 1998, Bioorganic & medicinal chemistry letters.
[32] Kotaro Terada,et al. In silico panning for a non-competitive peptide inhibitor , 2007, BMC Bioinformatics.
[33] P. Watt,et al. Screening for peptide drugs from the natural repertoire of biodiverse protein folds , 2006, Nature Biotechnology.
[34] François Stricher,et al. The FoldX web server: an online force field , 2005, Nucleic Acids Res..
[35] R. Glockshuber,et al. Infinite kinetic stability against dissociation of supramolecular protein complexes through donor strand complementation. , 2008, Structure.
[36] Gajendra P. S. Raghava,et al. SATPdb: a database of structurally annotated therapeutic peptides , 2015, Nucleic Acids Res..
[37] Baldomero Oliva,et al. Knowledge-based modeling of peptides at protein interfaces: PiPreD , 2015, Bioinform..
[38] Victor Neduva,et al. Peptides mediating interaction networks: new leads at last. , 2006, Current opinion in biotechnology.
[39] Anne Jacobson. Nanotechnology meets marine biology , 2002, Computing in Science & Engineering.
[40] David Baker,et al. Macromolecular modeling with rosetta. , 2008, Annual review of biochemistry.
[41] G. Crooks,et al. WebLogo: a sequence logo generator. , 2004, Genome research.
[42] T. Gibson,et al. Systematic Discovery of New Recognition Peptides Mediating Protein Interaction Networks , 2005, PLoS biology.
[43] A Tramontano,et al. Molecular model of the specificity pocket of the hepatitis C virus protease: implications for substrate recognition. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[44] Jack Snoeyink,et al. Almost-Delaunay simplices: Robust neighbor relations for imprecise 3D points using CGAL , 2007, Comput. Geom..