Abstract:
:A machine learning enhanced spectrum recognition system called spectrum recognition based on computer vision (SRCV) for data extraction from previously analyzed 13C and 1H NMR spectra has been developed. The intelligent system was designed with four function modules to extract data from three areas of NMR images, including 13C and 1H chemical shifts, the integral, and the range of the shift values. During this study, three machine learning models were pretrained for number recognition, which is the key procedure for NMR data extraction. The k nearest neighbor (kNN) method was selected with optimized k (k = 4), which displayed a 100% recognition rate. Subsequently, the performance of SRCV was tested and validated to have high accuracy with a short processing time (11-21 s) for each NMR spectral image. Our spectrum recognizer enables high-throughput 13C and 1H NMR data extraction from abundant spectra in the literature and has the potential to be used for spectral database construction. In addition, the system may be applicable to be developed for data import to computer-assisted structure elucidation systems, which would automate this procedure significantly. SRCV can be accessed in GitHub (https://github.com/WJmodels/SRCV).
journal_name
J Chem Inf Modeljournal_title
Journal of chemical information and modelingauthors
Jia W,Yang Z,Yang M,Cheng L,Lei Z,Wang Xdoi
10.1021/acs.jcim.0c01046subject
Has Abstractpub_date
2021-01-25 00:00:00pages
21-25issue
1eissn
1549-9596issn
1549-960Xjournal_volume
61pub_type
杂志文章abstract::Most physiological effects of thyroid hormones are mediated by the two thyroid hormone receptor subtypes, TRalpha and TRbeta. Several pharmacological effects mediated by TRbeta might be beneficial in important medical conditions such as obesity, hypercholesterolemia and diabetes, and selective TRbeta activation may el...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci900316e
更新日期:2009-11-01 00:00:00
abstract::SMIfp (SMILES fingerprint) is defined here as a scalar fingerprint describing organic molecules by counting the occurrences of 34 different symbols in their SMILES strings, which creates a 34-dimensional chemical space. Ligand-based virtual screening using the city-block distance CBD(SMIfp) as similarity measure provi...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci400206h
更新日期:2013-08-26 00:00:00
abstract::Calcium is involved in important intracellular processes, such as intracellular signaling from cell membrane receptors to the nucleus. Typically, calcium levels are kept at less than 100 nM in the nucleus and cytosol, but some calcium is stored in the endoplasmic reticulum (ER) lumen for rapid release to activate intr...
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
abstract::The molecular structure of four dimeric units (D-E, E-F, F-G, and G-H) of the DEFGH structural unit of heparin, their anionic forms, and their sodium salts have been studied using the B3LYP/6-31+G(d) method. The optimized geometries indicate that the most stable structure of these dimeric units in neutral state is sta...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci060060+
更新日期:2006-07-01 00:00:00
abstract::We present a theoretical study on the performance of ensemble docking methodologies considering multiple protein structures. We perform a theoretical analysis of pose prediction experiments which is completely unbiased, as we make no assumptions about specific scoring functions, search paradigms, protein structures, o...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci2002796
更新日期:2011-11-28 00:00:00
abstract::The solvation layer surrounding a protein is clearly an intrinsic part of protein structure-dynamics-function, and our understanding of how the hydration dynamics influences protein function is emerging. We have recently reported simulations indicating a correlation between regional hydration dynamics and the structur...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.9b00009
更新日期:2019-05-28 00:00:00
abstract::Modern industrial lubricants are often blended with an assortment of chemical additives to improve the performance of the base stock. Machine learning-based predictive models allow fast and veracious derivation of material properties and facilitate novel and innovative material designs. In this study, we outline the d...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.9b01068
更新日期:2020-03-23 00:00:00
abstract::Prediction of compound properties from structure via quantitative structure-activity relationship and machine-learning approaches is an important computational chemistry task in small-molecule drug research. Though many such properties are dependent on three-dimensional structures or even conformer ensembles, the majo...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.8b00151
更新日期:2018-05-29 00:00:00
abstract::Although there are several databases that contain data on many metabolites and reactions in biochemical pathways, there is still a big gap in the numbers between experimentally identified enzymes and metabolites. It is supposed that many catalytic enzyme genes are still unknown. Although there are previous studies tha...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.5b00216
更新日期:2016-03-28 00:00:00
abstract::Cyanobacterial fructose-1,6-/sedoheptulose-1,7-bisphoshatase (cy-FBP/SBPase) is a potential enzymatic target for screening of novel inhibitors that can combat harmful algal blooms. In the present study, we targeted the substrate binding pocket of cy-FBP/SBPase. A series of novel hit compounds from the SPECs database w...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci4007529
更新日期:2014-03-24 00:00:00
abstract::On the order of hundreds of absorption, distribution, metabolism, excretion, and toxicity (ADME/Tox) models have been described in the literature in the past decade which are more often than not inaccessible to anyone but their authors. Public accessibility is also an issue with computational models for bioactivity, a...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.5b00143
更新日期:2015-06-22 00:00:00
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 perfor...
journal_title:Journal of chemical information and modeling
pub_type: 信件
doi:10.1021/ci900047s
更新日期:2009-05-01 00:00:00
abstract::The large volume of protein-ligand structures now available enables innovative and efficient protocols in computational FBDD (Fragment-Based Drug Design) to be proposed based on experimental data. In this work, we build a database of MED-Portions, where a MED-Portion is a new structural object encoding protein-fragmen...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci8003094
更新日期:2009-02-01 00:00:00
abstract::Identifying sequence modifications that distinguish psychrophilic from mesophilic proteins is important for designing enzymes with different thermodynamic stabilities and to understand the underlying mechanisms. The PoPMuSiC algorithm is used to introduce, in silico, all the single-site mutations in four mesophilic an...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci050473v
更新日期:2006-05-01 00:00:00
abstract::The partitioning of solute molecules between immiscible solvents with significantly different polarities is of great importance. The polarization between the solute and solvent molecules plays an essential role in determining the solubility of the solute, which makes computational studies utilizing molecular mechanics...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.7b00001
更新日期:2017-10-23 00:00:00
abstract::Membrane fusion, a key step in the early stages of virus propagation, allows the release of the viral genome in the host cell cytoplasm. The process is initiated by fusion peptides that are small, hydrophobic components of viral membrane-embedded glycoproteins and are typically conserved within virus families. Here, w...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.0c01231
更新日期:2021-01-25 00:00:00
abstract::A phenotypic screen (PS) is used to identify compounds causing a desired phenotype in a complex biological system where mechanisms and targets are largely unknown. Deconvoluting the mechanism of action of actives and identification of relevant targets and pathways remains a formidable challenge. Current methods fail t...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci400245c
更新日期:2014-02-24 00:00:00
abstract::The study of chromatographic retention of natural products can be used to increase their identification speed in complex biological matrices. In this work, six variables were used to study the retention behavior in reversed phase liquid chromatography of 39 sesquiterpene lactones (SL) from an in-house database using c...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci500581q
更新日期:2015-01-26 00:00:00
abstract::The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In th...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.8b00148
更新日期:2018-06-25 00:00:00
abstract::The reuptake of neurotransmitters by dopamine, norepinephrine, and serotonin transporters during neuronal transmission requires a sodium gradient. An "ionic mode" of binding proposes that aspartate anchors the ligand's positive charge but ignores the direct role of sodium in ligand binding seen in the only representat...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci700255d
更新日期:2008-07-01 00:00:00
abstract::Factor Xa inhibitors are innovative anticoagulant agents that provide a better safety/efficacy profile compared to other anticoagulative drugs. A chemical feature-based modeling approach was applied to identify crucial pharmacophore patterns from 3D crystal structures of inhibitors bound to human factor Xa (Pdb entrie...
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
abstract::Retrieving molecules with specific structural features is a fundamental requirement of today's molecular database technologies. Estimates claim the chemical space relevant for drug discovery to be around 10⁶⁰ molecules. This figure is many orders of magnitude larger than the amount of molecules conventional databases ...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci400107k
更新日期:2013-07-22 00:00:00
abstract::The appropriate selection of a chemical space represented by the data set, the selection of its chemical data representation, the development of a correct modeling process using a robust and reproducible algorithm, and the performance of an exhaustive training and external validation determine the usability and reprod...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.7b00492
更新日期:2017-11-27 00:00:00
abstract::A database of about 700 high-resolution kinase structures was used to test the reliability of 17 docking procedures (using six docking software packages) by means of self- and cross-docking studies. The analysis of about 80 000 docking calculations suggests that the docking of an unknown ligand into a kinase has a pro...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci100161z
更新日期:2010-08-23 00:00:00
abstract::In the preceding paper (Duca, J. S.; Madison, V. S.; Voigt, J. H. J. Chem. Inf. Model. 2008, 48, 659-668), the accuracy of docking and affinity predictions of the Gold and Glide programs were investigated using single protein conformations spanning 150 CDK2/inhibitor crystallographic complexes. High docking accuracy w...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci700428d
更新日期:2008-03-01 00:00:00
abstract::MHC class II molecules bind peptides derived from extracellular proteins that have been ingested by antigen-presenting cells and display them to the immune system. Peptide loading occurs within the antigen-presenting cell and is facilitated by HLA-DM. HLA-DM stabilizes the open conformation of the MHCII binding groove...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.9b00104
更新日期:2019-06-24 00:00:00
abstract::The semiempirical quantum mechanical (SQM) methods used in drug design are commonly parametrized and tested on data sets of systems that may not be representative models for drug-biomolecule interactions in terms of both size and chemical composition. This is addressed here with a new benchmark data set, PLF547, deriv...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.9b01171
更新日期:2020-03-23 00:00:00
abstract::3-Hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is a primary target in the current clinical treatment of hypercholesterolemia with specific inhibitors of "statin" family. Statins are excellent inhibitors of the class I (human) enzyme but relatively poor inhibitors of the class II enzyme, which are well-known as...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci300163v
更新日期:2012-07-23 00:00:00
abstract::In this paper, we introduce the BiKi Life Sciences suite. This software makes it easy for computational medicinal chemists to run ad hoc molecular dynamics protocols in a novel and task-oriented environment; as a notebook, BiKi (acronym of Binding Kinetics) keeps memory of any activity together with dependencies among...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.7b00680
更新日期:2018-02-26 00:00:00
abstract::In this article, we present a systematic way to classify a family of high-genus fullerenes (HGFs) by decomposing them into two types of necklike structures, which are the negatively curved parts of parent toroidal carbon nanotubes. By replacing the faces of a uniform polyhedron with these necks, an HGF polyhedron corr...
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