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 design and training process of a general feed-forward artificial neural network that accurately predicts the dynamic viscosity of oil-based lubricant formulations. The network hyperparameters are systematically optimized by Bayesian optimization, and strongly correlated/collinear features are trimmed from the model. By harnessing domain knowledge in the selection of features, the quantitative structure-property relationship model is built with a relatively simple feature set and is versatile in predicting the dynamic viscosity of lubricant oils with and without enhancement by viscosity modifiers (VMs). Moreover, partial dependency, local-interpretable model-agnostic explanations, and Shapley values consistently show that the eccentricity index, Crippen MR, and Petitjean number are important predictors of viscosity. All in all, the neural model is reasonably accurate in predicting the dynamic viscosity of lubricant solvents and VM-enhanced lubricants with an R2 of 0.980 and 0.963, respectively.
journal_name
J Chem Inf Modeljournal_title
Journal of chemical information and modelingauthors
Loh GC,Lee HC,Tee XY,Chow PS,Zheng JWdoi
10.1021/acs.jcim.9b01068subject
Has Abstractpub_date
2020-03-23 00:00:00pages
1224-1234issue
3eissn
1549-9596issn
1549-960Xjournal_volume
60pub_type
杂志文章abstract：:All molecules of up to 11 atoms of C, N, O, and F possible under consideration of simple valency, chemical stability, and synthetic feasibility rules were generated and collected in a database (GDB). GDB contains 26.4 million molecules (110.9 million stereoisomers), including three- and four-membered rings and triple ...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci600423u
更新日期：2007-03-01 00:00:00
abstract：:Small-molecule protein docking is an essential tool in drug design and to understand molecular recognition. In the present work we introduce FlexAID, a small-molecule docking algorithm that accounts for target side-chain flexibility and utilizes a soft scoring function, i.e. one that is not highly dependent on specifi...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.5b00078
更新日期：2015-07-27 00:00:00
abstract：:The protonation states for nucleic acid bases are difficult to assess experimentally. In the context of DNA triplex, the protonation state of cytidine in the third strand is particularly important, because it needs to be protonated in order to form Hoogsteen hydrogen bonds. A sugar modification, locked nucleic acid (L...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.7b00741
更新日期：2018-04-23 00:00:00
abstract：:We present our newly developed and highly efficient lossless compression algorithm for trajectories of atom positions and volumetric data. The algorithm is designed as a two-step approach. In the first step, efficient polynomial extrapolation schemes reduce the information entropy of the data by exploiting both spatia...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.8b00501
更新日期：2018-10-22 00:00:00
abstract：:Most of the common molecular descriptors have numerous different implementations. This can influence the results of compound prioritization based on the multiparameter assessment (MPA) approach that allows a medicinal chemist to simultaneously analyze and achieve the desired balance of the diverse and often conflictin...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.7b00734
更新日期：2018-05-29 00:00:00
abstract：:The dissolution of a chemical into water is a process fundamental to both chemistry and biology. The persistence of a chemical within the environment and the effects of a chemical within the body are dependent primarily upon aqueous solubility. With the well-documented limitations hindering the accurate experimental d...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci900286s
更新日期：2009-11-01 00:00:00
abstract：:Novel statistical potentials derived from known protein structures are presented. They are designed to describe cation-pi and amino-pi interactions between a positively charged amino acid or an amino acid carrying a partially charged amino group and an aromatic moiety. These potentials are based on the propensity of r...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci050395b
更新日期：2006-03-01 00:00:00
abstract：:A new radial space-filling method for visualizing cluster hierarchies is presented. The method, referred to as a radial clustergram, arranges the clusters into a series of layers, each representing a different level of the tree. It uses adjacency of nodes instead of links to represent parent-child relationships and al...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci600427x
更新日期：2007-01-01 00:00:00
abstract：:An accurate scoring function is expected to correctly select the most stable structure from a set of pose candidates. One can hypothesize that a scoring function's ability to identify the most stable structure might be improved by emphasizing the most relevant atom pairwise interactions. However, it is hard to evaluat...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.9b00356
更新日期：2019-07-22 00:00:00
abstract：:We have performed a ligand coordinate analysis to monitor the movement of the inhibitor SC-558 from the active site of the COX-2 protein to the exterior using molecular dynamics techniques. This study provides an insight into the intermolecular interactions formed by the ligand during this journey. The published cryst...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci050142i
更新日期：2006-07-01 00:00:00
abstract：:Inhibition of plasmin has been found to effectively reduce fibrinolysis and to avoid hemorrhage. This can be achieved by addressing its kringle 1 domain with the known drug and lysine analogue tranexamic acid. Guided by shape similarities toward a previously discovered lead compound, 5-(4-piperidyl)isoxazol-3-ol, a se...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.7b00255
更新日期：2017-07-24 00:00:00
abstract：:Antimicrobial peptides (AMPs) have emerged as promising therapeutic alternatives to fight against the diverse infections caused by different pathogenic microorganisms. In this context, theoretical approaches in bioinformatics have paved the way toward the creation of several in silico models capable of predicting anti...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.5b00630
更新日期：2016-03-28 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
abstract：:This study has assessed the use of consensus regression, as compared to single multiple linear regression, models for the development of quantitative structure-activity relationships (QSARs). To provide a comparison, four data sets of varying size and complexity were analyzed: silastic membrane flux, toxicity of pheno...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci700016d
更新日期：2007-07-01 00:00:00
abstract：:Among the photophysical parameters that underpin Förster resonance energy transfer (FRET), perhaps the least explored is the spectral overlap term ( J). While by definition J increases linearly with acceptor molar absorption coefficient (ε(A) in M-1 cm-1), is proportional to wavelength (λ4), and depends on the degree ...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.8b00753
更新日期：2019-02-25 00:00:00
abstract：:The roles of chemical compounds in biological systems are now systematically analyzed by high-throughput experimental technologies. To automate the processing and interpretation of large-scale data it is necessary to develop bioinformatics methods to extract information from the chemical structures of these small mole...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci700006f
更新日期：2007-07-01 00:00:00
abstract：:Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics and biological research. The charge migration rate is controlled by the electronic couplings between the two nucleobases of DNA/RNA. These electronic coupling...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.0c01072
更新日期：2021-01-25 00:00:00
abstract：:We have studied the binding affinities of a set of 45 small-molecule inhibitors to protein tyrosine phosphatase 1B (PTP1B) through computational approaches. All of these compounds share a common oxalylamino benzoic acid (OBA) moiety. The complex structure of each compound was modeled by using the GOLD program plus the...
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
abstract：:The predictive performances of MC4PC were evaluated using its learning machine functionality. Its superior characteristics are demonstrated in this following up study using the newly published Ames mutagenicity benchmark set. ...
journal_title：Journal of chemical information and modeling
pub_type： 评论,信件
doi：10.1021/ci1000899
更新日期：2010-09-27 00:00:00
abstract：:In this work, we report an ab initio investigation based on density functional theory calculations within van der Waals D3 corrections to investigate the adsorption properties and activation of CO2 on transition-metal (TM) 13-atom clusters (TM = Ru, Rh, Pd, Ag), which is a key step for the development of subnano catal...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.9b00792
更新日期：2020-02-24 00:00:00
abstract：:The prediction of protein-ligand binding affinity has recently been improved remarkably by machine-learning-based scoring functions. For example, using a set of simple descriptors representing the atomic distance counts, the RF-Score improves the Pearson correlation coefficient to about 0.8 on the core set of the PDBb...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.7b00049
更新日期：2017-04-24 00:00:00
abstract：:Janus kinase 2 (JAK2) is a protein tyrosine kinase implicated in signaling by specific members of the cytokine receptor family. Although it has been established that the JAK2 tyrosine kinase is negatively regulated by the JAK homology 2 (JH2) pseudokinase domain, the underlying mechanism of JH2 mediated regulation rem...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci300308g
更新日期：2012-11-26 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
更新日期：2005-11-01 00:00:00
abstract：:Interfacial hydration strongly influences interactions between biomolecules. For example, drug-target complexes are often stabilized by hydration networks formed between hydrophilic residues and water molecules at the interface. Exhaustive exploration of hydration networks is challenging for experimental as well as th...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.5b00638
更新日期：2016-01-25 00:00:00
abstract：:Target-oriented substructure-based virtual screening (sSBVS) of molecules is a promising approach in drug discovery. Yet, there are doubts whether sSBVS is suitable also for extrapolation, that is, for detecting molecules that are very different from those used for training. Herein, we evaluate the predictive power of...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci200472s
更新日期：2012-03-26 00:00:00
abstract：:Classical nonpolarizable models, normally based on a combination of Lennard-Jones sites and point charges, are extensively used to model thermodynamic properties of fluids, including solvation. An important shortcoming of these models is that they do not explicitly account for polarization effects, i.e., a description...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/acs.jcim.9b01005
更新日期：2020-03-23 00:00:00
abstract：:Fragment complementation is gaining an increasing impact as a nonperturbing method to probe noncovalent interactions within protein supersecondary structures. In this study, the fast Fourier transform rigid-body docking algorithm ZDOCK has been employed for in silico reconstitution of the calcium binding protein calbi...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci0501995
更新日期：2005-09-01 00:00:00
abstract：:The efficiency of automated compound screening is heavily influenced by the design and the quality of the screening libraries used. We recently reported on the assembly of one diverse and one target-focused lead-like screening library. Using data from 15 enzyme-based screenings conducted using these libraries, their p...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci300382f
更新日期：2013-03-25 00:00:00
abstract：:We develop the idea that the use of ad hoc molecular descriptors in QSAR/QSPR studies is not an optimal solution. Instead, we propose to optimize these descriptors for the specific properties under study. In the case of topological indices (TIs) we propose the use of the generalized topological indices (GTIs), which a...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章
doi：10.1021/ci600448b
更新日期：2007-05-01 00:00:00
abstract：:This paper is an overview of the most significant and impactful interpretation approaches of quantitative structure-activity relationship (QSAR) models, their development, and application. The evolution of the interpretation paradigm from "model → descriptors → (structure)" to "model → structure" is indicated. The lat...
journal_title：Journal of chemical information and modeling
pub_type： 杂志文章,评审
doi：10.1021/acs.jcim.7b00274
更新日期：2017-11-27 00:00:00
