Abstract：
:The sensitivity of docking calculations to the geometry of the input ligand was studied. It was found that even small changes in the ligand input conformation can lead to large differences in the geometries and scores of the resulting docked poses. The accuracy of docked poses produced from different ligand input structures-the X-ray structure, the minimized Corina structure, and structures generated from conformational searches and molecular dynamics ensembles-were also assessed. It was found that using the X-ray ligand conformation as docking input does not always produce the most accurate docked pose when compared with other sources of ligand input conformations. Furthermore, no one method of conformer generation is guaranteed to always produce the most accurate docking pose. The docking scores are also highly sensitive to the source of the input conformation, which might introduce some noise in compound ranking and in binding affinity predictions. It is concluded that for the purposes of reproducibility and optimal performance, the most prudent procedure is to use multiple input structures for docking. The implications of these results on docking validation studies are discussed.
journal_name
J Chem Inf Modeljournal_title
Journal of chemical information and modelingauthors
Feher M,Williams CIdoi
10.1021/ci9000629subject
Has Abstractpub_date
2009-07-01 00:00:00pages
1704-14issue
7eissn
1549-9596issn
1549-960Xjournal_volume
49pub_type
杂志文章abstract：:Our main objective was to compile a data set of high-quality protein-fragment complexes and make it publicly available. Once assembled, the data set was challenged using docking procedures to address the following questions: (i) Can molecular docking correctly reproduce the experimentally solved structures? (ii) How t...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci2003363
更新日期：2011-11-28 00:00:00
abstract：:We investigate unexpectedly short non-covalent distances (<85% of the sum of van der Waals radii) in X-ray crystal structures of proteins. We curate over 11 000 high-quality protein crystal structures and an ultra-high-resolution (1.2 Å or better) subset containing >900 structures. Although our non-covalent distance c...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.9b00144
更新日期：2019-05-28 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci9001124
更新日期：2009-07-01 00:00:00
abstract：:The more that is known about human and other genome sequences and the correlation between gene expression and the course of a disease, the more evident it seems to be that DNA is chosen as a drug target instead of proteins which are built with the information encoded by DNA. According to this approach, small minor gro...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci600500v
更新日期：2007-07-01 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci500359e
更新日期：2015-04-27 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
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更新日期：2014-08-25 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
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更新日期：2014-06-23 00:00:00
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journal_title：Journal of chemical information and modeling
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
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更新日期：2011-07-25 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.0c00305
更新日期：2020-08-24 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci8004429
更新日期：2009-04-01 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
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更新日期：2017-07-24 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
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更新日期：2014-04-28 00:00:00
abstract：:Protein-protein interactions (PPIs) play vital roles in regulating biological processes, such as cellular and signaling pathways. Hotspots are certain residues located at protein-protein interfaces that contribute more in protein-protein binding than other residues. Research on the mutational effects of hotspots is im...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
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更新日期：2021-01-25 00:00:00
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journal_title：Journal of chemical information and modeling
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更新日期：2012-02-27 00:00:00
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journal_title：Journal of chemical information and modeling
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更新日期：2018-12-24 00:00:00
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journal_title：Journal of chemical information and modeling
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更新日期：2005-01-01 00:00:00
abstract：:Model lipid membranes made from binary mixtures of dimyristoylphosphatidylcholine/dipalmitoylphosphatidylcholine (DMPC/DPPC) and dimyristoylphosphatidylcholine/cholesterol (DMPC/Chol) exhibit coexistence of diverse lipid phases at appropriate temperature and composition. Since lipids in different phases show different...
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更新日期：2005-11-01 00:00:00
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journal_title：Journal of chemical information and modeling
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更新日期：2018-04-23 00:00:00
abstract：:The quantitative structure-activity relationship (QSAR) approach has been used to model a wide range of chemical-induced biological responses. However, it had not been utilized to model chemical-induced genomewide gene expression changes until very recently, owing to the complexity of training and evaluating a very la...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
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更新日期：2017-09-25 00:00:00
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更新日期：2011-01-24 00:00:00
abstract：:CDC25 phosphatases play critical roles in cell cycle regulation and are attractive targets for anticancer therapies. Several small non-peptide molecules are known to inhibit CDC25, but many of them appear to form a covalent bond with the enzyme or act through oxidation of the thiolate group of the catalytic cysteine. ...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
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更新日期：2008-01-01 00:00:00
abstract：:The protection exerted by 3,5-dihydroxy-4-methoxybenzyl alcohol (DHMBA), a phenolic compound recently isolated from the Pacific oyster, against oxidative stress (OS) is investigated using the density functional theory. Our results indicate that DHMBA is an outstanding peroxyl radical scavenger, being about 15 times an...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
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更新日期：2015-12-28 00:00:00
