Abstract：
:Small molecule flexible alignment is a critical component of both ligand- and structure-based methods in computer-aided drug discovery. Despite its importance, the availability of high-quality flexible alignment software packages is limited. Here, we present BCL::MolAlign, a freely available property-based molecular alignment program. BCL::MolAlign accommodates ligand flexibility through a combination of pregenerated conformers and on-the-fly bond rotation. BCL::MolAlign converges on alignment poses by sampling the relative orientations of mutually matching atom pairs between molecules through Monte Carlo Metropolis sampling. Across six diverse ligand data sets, BCL::MolAlign flexible alignment outperforms MOE, ROCS, and FLEXS in recovering native ligand binding poses. Moreover, the BCL::MolAlign alignment score is more predictive of ligand activity than maximum common substructure similarity across 10 data sets. Finally, on a recently published benchmark set of 20 high quality congeneric ligand-protein complexes, BCL::MolAlign is able to recover a larger fraction of native binding poses than maximum common substructure-based alignment and RosettaLigand. BCL::MolAlign can be obtained as part of the Biology and Chemistry Library (BCL) software package freely with an academic license or can be accessed via Web server at http://meilerlab.org/index.php/servers/molalign .
journal_name
J Chem Inf Modeljournal_title
Journal of chemical information and modelingauthors
Brown BP,Mendenhall J,Meiler Jdoi
10.1021/acs.jcim.9b00020subject
Has Abstractpub_date
2019-02-25 00:00:00pages
689-701issue
2eissn
1549-9596issn
1549-960Xjournal_volume
59pub_type
杂志文章abstract：:Functional diversity of the three-finger-protein domain (TFPD) had been acquired via hypervariability of some sequence positions and extensive insertion/deletion of short AA-segments that caused multidimensional drift of several sequence attributes such as the overall (HI) and local hydrophobicity levels, the isoelect...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.5b00322
更新日期：2015-09-28 00:00:00
abstract：:Accurate hydrogen placement in molecular modeling is crucial for studying the interactions and dynamics of biomolecular systems. The carboxyl functional group is a prototypical example of a functional group that requires protonation during structure preparation. To our knowledge, when in their neutral form, carboxylic...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.8b00835
更新日期：2019-05-28 00:00:00
abstract：:One tactic for cysteine protease inhibition is to form a covalent bond between an electrophilic atom of the inhibitor and the thiol of the catalytic cysteine. In this study, we evaluate the reaction free energy obtained from a hybrid quantum mechanical/molecular mechanical (QM/MM) free energy profile as a predictor of...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.9b00847
更新日期：2020-02-24 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.0c00945
更新日期：2020-12-28 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.5b00543
更新日期：2015-10-26 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.7b00241
更新日期：2017-08-28 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.6b00595
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.0c00985
更新日期：2021-01-21 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci400233j
更新日期：2013-09-23 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci400587f
更新日期：2014-01-27 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.0c00598
更新日期：2021-01-25 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci7001507
更新日期：2007-09-01 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci500556k
更新日期：2014-12-22 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci049778k
更新日期：2005-01-01 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.7b00227
更新日期：2018-01-22 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：2011-06-27 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci060164k
更新日期：2007-01-01 00:00:00
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journal_title：Journal of chemical information and modeling
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doi：10.1021/ci5005898
更新日期：2015-01-26 00:00:00
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journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci200311w
更新日期：2011-10-24 00:00:00
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journal_title：Journal of chemical information and modeling
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更新日期：2006-11-01 00:00:00
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journal_title：Journal of chemical information and modeling
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更新日期：2006-03-01 00:00:00
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更新日期：2014-02-24 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：2020-08-24 00:00:00
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更新日期：2013-08-26 00:00:00
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journal_title：Journal of chemical information and modeling
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更新日期：2005-03-01 00:00:00
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journal_title：Journal of chemical information and modeling
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更新日期：2018-01-22 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
pub_type： 杂志文章
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更新日期：2020-02-24 00:00:00
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journal_title：Journal of chemical information and modeling
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更新日期：2005-05-01 00:00:00
