Zobrazeno 1 - 10
of 810
pro vyhledávání: '"Searching the conformational space for docking"'
Autor:
Paweł Śledź, Amedeo Caflisch
Publikováno v:
Current Opinion in Structural Biology. 48:93-102
Recent years have witnessed rapid developments of computer-aided drug design methods, which have reached accuracy that allows their routine practical applications in drug discovery campaigns. Protein structure-based methods are useful for the predict
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::14402df34f00ec81ff61ae76c1f38852
https://doi.org/10.1016/j.sbi.2017.10.010
https://doi.org/10.1016/j.sbi.2017.10.010
Publikováno v:
Journal of Molecular Graphics and Modelling. 78:139-147
Discovery of new inhibitors of the protein associated with a given disease is the initial and most important stage of the whole process of the rational development of new pharmaceutical substances. New inhibitors block the active site of the target p
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5804cab2b95b16b5b101609849270b42
https://doi.org/10.1016/j.jmgm.2017.10.007
https://doi.org/10.1016/j.jmgm.2017.10.007
Publikováno v:
Journal of Computer-Aided Molecular Design
Advanced molecular docking methods often aim at capturing the flexibility of the protein upon binding to the ligand. In this study, we investigate whether instead a simple rigid docking method can be applied, if combined with multiple target structur
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::dbcc0fc55e75ff0b39ea47f4c1b32d51
https://doi.org/10.1007/s10822-017-0074-x
https://doi.org/10.1007/s10822-017-0074-x
Publikováno v:
Journal of Molecular Graphics and Modelling. 76:128-135
In order to design novel non-peptidic inhibitors of BACE1, many research groups have attempted using computational studies including docking analyses. Since there are too many 3D structures for BACE1 in the protein database, the selection of suitable
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::fd6927000ce32a94b0fe58c2373d80cb
https://doi.org/10.1016/j.jmgm.2017.06.023
https://doi.org/10.1016/j.jmgm.2017.06.023
Autor:
Michal Brylinski
Publikováno v:
Chemical Biology & Drug Design. 91:380-390
The ability to design and fine-tune non-covalent interactions between organic ligands and proteins is indispensable to rational drug development. Aromatic stacking has long been recognized as one of the key constituents of ligand-protein interfaces.
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::28a3971ed185f6339c0f81bd16908e59
https://doi.org/10.1111/cbdd.13084
https://doi.org/10.1111/cbdd.13084
Publikováno v:
Journal of Molecular Graphics and Modelling. 75:241-249
c-Met is a transmembrane receptor tyrosine kinase and an important therapeutic target for anticancer drugs. In the present study, we systematically investigated the influence of a range of parameters on the correlation between experimental and calcul
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3766d5a6e9ef6e3c3fd7933de1a3daad
https://doi.org/10.1016/j.jmgm.2017.04.004
https://doi.org/10.1016/j.jmgm.2017.04.004
Autor:
Mateusz Kurcinski, Maciej Blaszczyk, Maciej Pawel Ciemny, Andrzej Kolinski, Sebastian Kmiecik
Publikováno v:
BioMedical Engineering OnLine, Vol 16, Iss S1, Pp 1-9 (2017)
BioMedical Engineering
BioMedical Engineering
Many protein–protein interactions are mediated by a short linear motif. Usually, amino acid sequences of those motifs are known or can be predicted. It is much harder to experimentally characterize or predict their structure in the bound form. In t
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0ebfd7ccdcc4602c11c8ea4cd5521d97
http://link.springer.com/article/10.1186/s12938-017-0362-7
http://link.springer.com/article/10.1186/s12938-017-0362-7
Publikováno v:
Journal of Chemical Information and Modeling. 57:1691-1702
Docking simulations are very popular approaches able to assess the capacity of a given ligand to interact with a target. Docking simulations are usually focused on a single best complex even though many studies showed that ligands retain a significan
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3eda463625f625681352262a12f92241
https://doi.org/10.1021/acs.jcim.7b00121
https://doi.org/10.1021/acs.jcim.7b00121
Publikováno v:
Journal of Computer-Aided Molecular Design. 31:689-699
The growing number of protein-ligand complex structures, particularly the structures of proteins co-bound with different ligands, in the Protein Data Bank helps us tackle two major challenges in molecular docking studies: the protein flexibility and
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ad7235f458dd044a3b2fc633239334c1
https://doi.org/10.1007/s10822-017-0038-1
https://doi.org/10.1007/s10822-017-0038-1
Autor:
D. Sam Paul, Namasivayam Gautham
Publikováno v:
Journal of Molecular Graphics and Modelling. 74:89-99
We have earlier reported the MOLSDOCK technique to perform rigid receptor/flexible ligand docking. The method uses the MOLS method, developed in our laboratory. In this paper we report iMOLSDOCK, the ‘flexible receptor’ extension we have carried
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b54e0390979d572b0ea5ccd59065cd21
https://doi.org/10.1016/j.jmgm.2017.03.008
https://doi.org/10.1016/j.jmgm.2017.03.008