Abstract:
:The spatial sign is a multivariate extension of the concept of sign. Recently multivariate estimators of covariance structures based on spatial signs have been examined by various authors. These new estimators are found to be robust to outlying observations. From a computational point of view, estimators based on spatial sign are very easy to implement as they boil down to a transformation of the data to their spatial signs, from which the classical estimator is then computed. Hence, one can also consider the transformation to spatial signs to be a preprocessing technique, which ensures that the calibration procedure as a whole is robust. In this paper, we examine the special case of spatial sign preprocessing in combination with partial least squares regression as the latter technique is frequently applied in the context of chemical data analysis. In a simulation study, we compare the performance of the spatial sign transformation to nontransformed data as well as to two robust counterparts of partial least squares regression. It turns out that the spatial sign transform is fairly efficient but has some undesirable bias properties. The method is applied to a recently published data set in the field of quantitative structure-activity relationships, where it is seen to perform equally well as the previously described best linear model for these data.
journal_name
J Chem Inf Modeljournal_title
Journal of chemical information and modelingauthors
Serneels S,De Nolf E,Van Espen PJdoi
10.1021/ci050498usubject
Has Abstractpub_date
2006-05-01 00:00:00pages
1402-9issue
3eissn
1549-9596issn
1549-960Xjournal_volume
46pub_type
杂志文章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 primary goal of ligand-based virtual screening is to identify active compounds consisting of a core scaffold that is not found in the current active compound pool. Scaffold hopping is the term used for this purpose. In the present study, topological representations of pharmacophore features on chemical graphs were...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.0c00098
更新日期:2020-04-27 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::In a departure from conventional chemical approaches, data-driven models of chemical reactions have recently been shown to be statistically successful using machine learning. These models, however, are largely black box in character and have not provided the kind of chemical insights that historically advanced the fie...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.9b00721
更新日期:2020-03-23 00:00:00
abstract::The worldwide increase and proliferation of drug resistant microbes, coupled with the lag in new drug development, represents a major threat to human health. In order to reduce the time and cost for exploring the chemical search space, drug discovery increasingly relies on computational biology approaches. One key ste...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.0c00075
更新日期:2020-06-22 00:00:00
abstract::The urgent need for new treatments for the chronic lung disease idiopathic pulmonary fibrosis (IPF) motivates research into antagonists of the RGD binding integrin αvβ6, a protein linked to the initiation and progression of the disease. Molecular dynamics (MD) simulations of αvβ6 in complex with its natural ligand, pr...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.0c00254
更新日期:2020-11-23 00:00:00
abstract::Throughout the drug discovery process, discovery teams are compelled to use statistics for making decisions using data from a variety of inputs. For instance, teams are asked to prioritize compounds for subsequent stages of the drug discovery process, given results from multiple screens. To assist in the prioritizatio...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci600556v
更新日期:2007-05-01 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::We propose an improved solvent contact model to estimate the solvation free energy of an organic molecule from individual atomic contributions. The modification of the solvation model involves the optimization of three kinds of parameters in the solvation free energy function: atomic fragmental volume, maximum atomic ...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci600453b
更新日期:2007-03-01 00:00:00
abstract::Whereas 400 million distinct compounds are now purchasable within the span of a few weeks, the biological activities of most are unknown. To facilitate access to new chemistry for biology, we have combined the Similarity Ensemble Approach (SEA) with the maximum Tanimoto similarity to the nearest bioactive to predict a...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.7b00316
更新日期:2018-01-22 00:00:00
abstract::A data set of 130 diverse compounds containing both central nervous system (CNS) and non-CNS drugs was used to generate a renal clearance model using a classical Volsurf approach. Percentage renal clearance data was used as a biological input. The score plots obtained from principal component analysis and partial leas...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci0503309
更新日期:2006-05-01 00:00:00
abstract::Aminoglycosides are antibiotics targeting the 16S RNA A site of the bacterial ribosome. There have been many efforts directed toward design of their synthetic derivatives, however with only few successes. As RNA binders, aminoglycosides are also a difficult target for computational drug design, since most of the exist...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci800361a
更新日期:2009-02-01 00:00:00
abstract::Flavonoids, the vastest class of natural polyphenols, are extensively investigated for their multiple benefits on human health. Due to their physicochemical or biological properties, many representatives are considered to exhibit low selectivity among various protein targets or to plague high-throughput screening (HTS...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci5002668
更新日期:2014-08-25 00:00:00
abstract::Metabolic stability is an important property of drug molecules that should-optimally-be taken into account early on in the drug design process. Along with numerous medium- or high-throughput assays being implemented in early drug discovery, a prediction tool for this property could be of high value. However, metabolic...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci700142c
更新日期:2008-04-01 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
abstract::Ionotropic glutamate receptors (iGluRs) are synaptic proteins that facilitate signal transmission in the central nervous system. Extracellular iGluR cleft closure is linked to receptor activation; however, the mechanism underlying partial agonism is not entirely understood. Full agonists close the bilobed ligand-bindi...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci2000055
更新日期:2011-05-23 00:00:00
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 a...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.9b00020
更新日期:2019-02-25 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 community structure-activity resource (CSAR) data sets are used to develop and test a support vector machine-based scoring function in regression mode (SVR). Two scoring functions (SVR-KB and SVR-EP) are derived with the objective of reproducing the trend of the experimental binding affinities provided within the ...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci200078f
更新日期:2011-09-26 00:00:00
abstract::New molecular descriptors, RED (Renyi entropy descriptors), based on the generalized entropies introduced by Renyi are presented. Topological descriptors based on molecular features have proven to be useful for describing molecular profiles. Renyi entropy is used as a variability measure to contract a feature-pair dis...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci900275w
更新日期:2009-11-01 00:00:00
abstract::Pharmacophore search is a key component of many drug discovery efforts. Pharmer is a new computational approach to pharmacophore search that scales with the breadth and complexity of the query, not the size of the compound library being screened. Two novel methods for organizing pharmacophore data, the Pharmer KDB-tre...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci200097m
更新日期:2011-06-27 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::DNA damage alters genetic information and adversely affects gene expression pathways leading to various complex genetic disorders and cancers. DNA repair proteins recognize and rectify DNA damage and mismatches with high fidelity. A critical molecular event that occurs during most protein-mediated DNA repair processes...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.7b00636
更新日期:2018-03-26 00:00:00
abstract::A homology model of the Arabidopsis thaliana UV resistance locus 8 (UVR8) protein is presented herein, showing a seven-bladed β-propeller conformation similar to the globular structure of RCC1. The UVR8 amino acid sequence contains a very high amount of conserved tryptophans, and the homology model shows that seven of...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci200017f
更新日期:2011-06-27 00:00:00
abstract::We report a novel method called ADAN (Applicability Domain ANalysis) for assessing the reliability of drug property predictions obtained by in silico methods. The assessment provided by ADAN is based on the comparison of the query compound with the training set, using six diverse similarity criteria. For every criteri...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci500172z
更新日期:2014-05-27 00:00:00
abstract::A model for prediction of percent intestinal absorption (%Abs) of neutral molecules was developed based upon surface charges of the molecule calculated by density functional theory (DFT). The surface charges are decomposed into sigma moments which are correlated to a partition coefficient representing transfer of the ...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci049653f
更新日期:2005-09-01 00:00:00
abstract::Traditional herbal medicine has been an inseparable part of the traditional medical science in many countries throughout history. Nowadays, the popularity of using herbal medicines in daily life, as well as clinical practices, has gradually expanded to numerous Western countries with positive impacts and acceptance. T...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/acs.jcim.9b00826
更新日期:2020-03-23 00:00:00
abstract::CYP19A1, also known as aromatase or estrogen synthetase, is the rate-limiting enzyme in the biosynthesis of estrogens from their corresponding androgens. Several clinically used breast cancer therapies target aromatase. In this work, explicitly solvated all-atom molecular dynamics simulations of aromatase with a model...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci400225w
更新日期:2013-08-26 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
abstract::Resonance structures of polycyclic aromatic hydrocarbons can be associated with numerical formulas by assigning pi-electrons of C=C double bonds to individual benzenoid rings. Each C=C double bond in a resonance structure assigns two pi-electrons to a ring in a fused-benzenoid system if it is not shared by adjacent ri...
journal_title:Journal of chemical information and modeling
pub_type: 杂志文章
doi:10.1021/ci050196s
更新日期:2006-01-01 00:00:00