Abstract：
:A database has been derived from recently reported [60]fullerene derivatives, and their binding scores with HIV-1 PR have been computed using docking techniques. Computational methods have been used to predict which derivatives may have high binding affinities, and for these compounds biological tests have been performed with purified PR. Experimental results confirm the high binding scores of fullerene derivatives predicted from the docking calculations. Our measurements showed that the fullerene derivative (Fmoc-Baa) has about three times better inhibitory binding (K(i) = 36 nM) than the most active fullerene-based inhibitor (K(i) = 103 nM) currently available.
journal_name
J Chem Inf Modeljournal_title
Journal of chemical information and modelingauthors
Durdagi S,Supuran CT,Strom TA,Doostdar N,Kumar MK,Barron AR,Mavromoustakos T,Papadopoulos MGdoi
10.1021/ci900047ssubject
Has Abstractpub_date
2009-05-01 00:00:00pages
1139-43issue
5eissn
1549-9596issn
1549-960Xjournal_volume
49pub_type
信件abstract：:An important issue in developing protein-ligand docking methods is how to incorporate receptor flexibility. Consideration of receptor flexibility using an ensemble of precompiled receptor conformations or by employing an effectively enlarged binding pocket has been reported to be useful. However, direct consideration ...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci300342z
更新日期：2012-12-21 00:00:00
abstract：:Virtual screening (VS) can be accomplished in either ligand- or structure-based methods. In recent times, an increasing number of 2D fingerprint and 3D shape similarity methods have been used in ligand-based VS. To evaluate the performance of these ligand-based methods, retrospective VS was performed on a tailored dir...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci300030u
更新日期：2012-05-25 00:00:00
abstract：:In this work, we present a systematical investigation of the influence of ligand protonation states, stereoisomers, and tautomers on results obtained with the two protein-ligand docking programs GOLD and PLANTS. These different states were generated with a fully automated tool, called SPORES (Structure PrOtonation and...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci800420z
更新日期：2009-06-01 00:00:00
abstract：:In this study, we aimed to develop a new ligand-based virtual screening approach using an effective shape-overlapping procedure and a more robust scoring function (denoted by the HWZ score for convenience). The HWZ score-based virtual screening approach was tested against the compounds for 40 protein targets available...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci200617d
更新日期：2012-04-23 00:00:00
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journal_title：Journal of chemical information and modeling
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doi：10.1021/ci3001919
更新日期：2012-08-27 00:00:00
abstract：:We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables ...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci050216q
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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
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更新日期：2010-11-22 00:00:00
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journal_title：Journal of chemical information and modeling
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更新日期：2020-02-24 00:00:00
abstract：:The human androgen receptor (AR) is a ligand-activated transcription factor that plays a pivotal role in the development and progression of prostate cancer (PCa). Many forms of castration-resistant prostate cancer (CRPC) still rely on the AR for survival. Currently used antiandrogens face clinical limitations as drug ...
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
doi：10.1021/acs.jcim.6b00493
更新日期：2016-10-24 00:00:00
abstract：:Binding affinity prediction with implicit solvent models remains a challenge in virtual screening for drug discovery. In order to assess the predictive power of implicit solvent models in docking techniques with Amber scoring, three generalized Born models (GBHCT, GBOBCI, and GBOBCII) available in Dock 6.7 were utiliz...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.6b00418
更新日期：2016-10-24 00:00:00
abstract：:Growing data sets with increased time for analysis is hampering predictive modeling in drug discovery. Model building can be carried out on high-performance computer clusters, but these can be expensive to purchase and maintain. We have evaluated ligand-based modeling on cloud computing resources where computations ar...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci500580y
更新日期：2015-01-26 00:00:00
abstract：:Optimization of ligand binding affinity to the target protein of interest is a primary objective in small-molecule drug discovery. Until now, the prediction of binding affinities by computational methods has not been widely applied in the drug discovery process, mainly because of its lack of accuracy and reproducibili...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.6b00780
更新日期：2017-04-24 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.6b00347
更新日期：2016-10-24 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.6b00475
更新日期：2017-02-27 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci800313h
更新日期：2009-04-01 00:00:00
abstract：:The d-Ala:d-Lac ligase, VanA, plays a critical role in the resistance of vancomycin. Indeed, it is involved in the synthesis of a peptidoglycan precursor, to which vancomycin cannot bind. The reaction catalyzed by VanA requires the opening of the so-called "ω-loop", so that the substrates can enter the active site. He...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.6b00211
更新日期：2016-09-26 00:00:00
abstract：:Different forms of synaptic plasticity in the cerebellum expressed at the synapses onto Purkinje cells (PCs) are mediated by membrane metabotropic glutamate receptors (mGluRs). There are three main mGluR groups with a total of 8 subtypes. Although mGluRs are also found at the climbing fiber (CF) to PC synapses, the di...
journal_title：Journal of chemical information and modeling
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doi：10.1021/ci050161s
更新日期：2005-11-01 00:00:00
abstract：:This study examines the dependence of molecular alignment accuracy on a variety of factors including the choice of molecular template, alignment method, conformational flexibility, and type of protein target. We used eight test systems for which X-ray data on 145 ligand-protein complexes were available. The use of X-r...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci060134h
更新日期：2006-09-01 00:00:00
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journal_title：Journal of chemical information and modeling
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更新日期：2014-10-27 00:00:00
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journal_title：Journal of chemical information and modeling
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更新日期：2019-03-25 00:00:00
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journal_title：Journal of chemical information and modeling
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更新日期：2019-09-23 00:00:00
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journal_title：Journal of chemical information and modeling
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更新日期：2020-03-23 00:00:00
abstract：:To promote more productive combinatorial endeavors, the Diversity Space methodology introduced here enables similarity comparisons at the library level. Particularly at an early screening stage, when little or no information is available regarding the pharmacophoric entities necessary for binding, it is more efficient...
journal_title：Journal of chemical information and modeling
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更新日期：2006-07-01 00:00:00
abstract：:A MMGBSA variant (here referred to as Nwat-MMGBSA), based on the inclusion of a certain number of explicit water molecules (Nwat) during the calculations, has been tested on a set of 20 protein-protein complexes, using the correlation between predicted and experimental binding energy as the evaluation metric. Besides ...
journal_title：Journal of chemical information and modeling
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doi：10.1021/acs.jcim.6b00196
更新日期：2016-09-26 00:00:00
abstract：:Cytochrome P450 3A4 metabolizes nearly 50% of the drugs currently in clinical use with a broad range of substrate specificity. Early prediction of metabolites of xenobiotic compounds is crucial for cost efficient drug discovery and development. We developed a new combined model, MLite, for the prediction of regioselec...
journal_title：Journal of chemical information and modeling
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更新日期：2008-03-01 00:00:00
abstract：:With the hope of discovering effective analgesics with fewer side effects, attention has recently shifted to allosteric modulators of the opioid receptors. In the past two years, the first chemotypes of positive or silent allosteric modulators (PAMs or SAMs, respectively) of μ- and δ-opioid receptor types have been re...
journal_title：Journal of chemical information and modeling
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更新日期：2015-09-28 00:00:00
abstract：:The momentum gained by research on biologics has not been met yet with equal thrust on the informatics side. There is a noticeable lack of software for data management that empowers the bench scientists working on the development of biologic therapeutics. SARvision|Biologics is a tool to analyze data associated with b...
journal_title：Journal of chemical information and modeling
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更新日期：2013-10-28 00:00:00
abstract：:Visualizing high-dimensional data by projecting them into a two- or three-dimensional space is a popular approach in many scientific fields, including computer-aided drug design and cheminformatics. In contrast, dimensionality reduction techniques have been far less explored for materials informatics. Nevertheless, si...
journal_title：Journal of chemical information and modeling
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更新日期：2018-12-24 00:00:00
