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 thorough must the sampling be to replicate the experimental data? (iii) Can commonly used scoring functions discriminate between the native pose and other energy minima? The data set, named SERAPhiC (Selected Fragment Protein Complexes), is publicly available in a ready-to-dock format ( http://www.iit.it/en/drug-discovery-and-development/seraphic.html ). It offers computational medicinal chemists a reliable test set for both in silico protocol assessment and software development.
journal_name
J Chem Inf Modeljournal_title
Journal of chemical information and modelingauthors
Favia AD,Bottegoni G,Nobeli I,Bisignano P,Cavalli Adoi
10.1021/ci2003363subject
Has Abstractpub_date
2011-11-28 00:00:00pages
2882-96issue
11eissn
1549-9596issn
1549-960Xjournal_volume
51pub_type
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journal_title：Journal of chemical information and modeling
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journal_title：Journal of chemical information and modeling
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journal_title：Journal of chemical information and modeling
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journal_title：Journal of chemical information and modeling
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更新日期：2014-08-25 00:00:00
abstract：:Determination of structural similarities between protein binding pockets is an important challenge in in silico drug design. It can help to understand selectivity considerations, predict unexpected ligand cross-reactivity, and support the putative annotation of function to orphan proteins. To this end, Cavbase was dev...
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journal_title：Journal of chemical information and modeling
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journal_title：Journal of chemical information and modeling
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更新日期：2013-02-25 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
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abstract：:Maltose-binding protein is a periplasmic binding protein responsible for transport of maltooligosaccarides through the periplasmic space of Gram-negative bacteria, as a part of the ABC transport system. The molecular mechanisms of the initial ligand binding and induced large scale motion of the protein's domains still...
journal_title：Journal of chemical information and modeling
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doi：10.1021/ci500520q
更新日期：2015-02-23 00:00:00
abstract：:Glycan Optimized Dual Empirical Spectrum Simulation (GODESS) is a web service, which has been recently shown to be one of the most accurate tools for simulation of (1)H and (13)C 1D NMR spectra of natural carbohydrates and their derivatives. The new version of GODESS supports visualization of the simulated (1)H and (1...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.6b00083
更新日期：2016-06-27 00:00:00
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journal_title：Journal of chemical information and modeling
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doi：10.1021/acs.jcim.9b00619
更新日期：2020-09-28 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.7b00223
更新日期：2017-09-25 00:00:00
abstract：:Insect neuropeptide receptors, including allatostatin receptor type C (AstR-C), a G protein-coupled receptor, are among the potential targets for designing next-generation pesticides that despite their importance in offering a new mode-of-action have been overlooked. Focusing on AstR-C of Thaumetopoea pityocampa, a co...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.0c00985
更新日期：2021-01-21 00:00:00
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journal_title：Journal of chemical information and modeling
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doi：10.1021/acs.jcim.7b00398
更新日期：2018-05-29 00:00:00
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更新日期：2007-07-01 00:00:00
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更新日期：2020-08-24 00:00:00
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更新日期：2007-05-01 00:00:00
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更新日期：2009-03-01 00:00:00
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journal_title：Journal of chemical information and modeling
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更新日期：2009-11-01 00:00:00
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journal_title：Journal of chemical information and modeling
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更新日期：2009-02-01 00:00:00
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journal_title：Journal of chemical information and modeling
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