TY - JOUR
T1 - DINC 2.0
T2 - A new protein-peptide docking webserver using an incremental approach
AU - Antunes, Dinler A.
AU - Moll, Mark
AU - Devaurs, Didier
AU - Jackson, Kyle R.
AU - Lizée, Gregory
AU - Kavraki, Lydia E.
N1 - Funding Information:
Work on this project by D.A. Antunes, L.E. Kavraki, M. Moll, G. Lizée, and K.R. Jackson was supported by NIH R21CA209941-01 (co-PIs: L.E. Kavraki and G. Lizée) through the Informatics Technology for Cancer Research (ITCR) initiative of the NCI. Work on this project by D. Devaurs was supported by a training fellowship from the Gulf Coast Consortia, on the Computational Cancer Biology Training Program (CPRIT grant no. RP170593, PI: M. Pettitt).
Publisher Copyright:
© 2017 American Association for Cancer Research.
PY - 2017/11/1
Y1 - 2017/11/1
N2 - Molecular docking is a standard computational approach to predict binding modes of protein-ligand complexes by exploring alternative orientations and conformations of the ligand (i.e., by exploring ligand flexibility). Docking tools are largely used for virtual screening of small drug-like molecules, but their accuracy and efficiency greatly decays for ligands with more than 10 flexible bonds. This prevents a broader use of these tools to dock larger ligands, such as peptides, which are molecules of growing interest in cancer research. To overcome this limitation, our group has previously proposed a metadocking strategy, called DINC, to predict binding modes of large ligands. By incrementally docking overlapping fragments of a ligand, DINC allowed predicting binding modes of peptide- based inhibitors of transcription factors involved in cancer. Here, we describe DINC 2.0, a revamped version of the DINC webserver with enhanced capabilities and a more user-friendly interface. DINC 2.0 allows docking ligands that were previously too challenging for DINC, such as peptides with more than 25 flexible bonds. The webserver is freely accessible at http:// dinc.kavrakilab.org, together with additional documentation and video tutorials. Our team will provide continuous support for this tool and is working on extending its applicability to other challenging fields, such as personalized immunotherapy against cancer. Cancer Res; 77(21); e55-57.
AB - Molecular docking is a standard computational approach to predict binding modes of protein-ligand complexes by exploring alternative orientations and conformations of the ligand (i.e., by exploring ligand flexibility). Docking tools are largely used for virtual screening of small drug-like molecules, but their accuracy and efficiency greatly decays for ligands with more than 10 flexible bonds. This prevents a broader use of these tools to dock larger ligands, such as peptides, which are molecules of growing interest in cancer research. To overcome this limitation, our group has previously proposed a metadocking strategy, called DINC, to predict binding modes of large ligands. By incrementally docking overlapping fragments of a ligand, DINC allowed predicting binding modes of peptide- based inhibitors of transcription factors involved in cancer. Here, we describe DINC 2.0, a revamped version of the DINC webserver with enhanced capabilities and a more user-friendly interface. DINC 2.0 allows docking ligands that were previously too challenging for DINC, such as peptides with more than 25 flexible bonds. The webserver is freely accessible at http:// dinc.kavrakilab.org, together with additional documentation and video tutorials. Our team will provide continuous support for this tool and is working on extending its applicability to other challenging fields, such as personalized immunotherapy against cancer. Cancer Res; 77(21); e55-57.
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U2 - 10.1158/0008-5472.CAN-17-0511
DO - 10.1158/0008-5472.CAN-17-0511
M3 - Article
C2 - 29092940
AN - SCOPUS:85035057971
SN - 0008-5472
VL - 77
SP - e55-e57
JO - Cancer Research
JF - Cancer Research
IS - 21
ER -