abstract：:The [H2X2]+ (X = Cl, Br) formula could refer to two possible stable structures, namely, the hydrogen-bonded complex and the three-electron-bonded one. In contrary to the results published by other authors, we claim that for the F-type structures the hydrogen-bonded form is the only possible one and the [HFFH]+ complex...

journal_title：Journal of chemical information and modeling

authors： Bil A,Berski S,Latajka Z

更新日期：2007-05-01 00:00:00

abstract：:The programs Phase and Catalyst HypoGen are compared for their performance in determining three-dimensional quantitative structure-activity relationships. Eight sets of compounds with measured activity were collected from the public literature and partitioned into suitable training and test sets by an automated proced...

journal_title：Journal of chemical information and modeling

authors： Evans DA,Doman TN,Thorner DA,Bodkin MJ

更新日期：2007-05-01 00:00:00

abstract：:Ab initio quantum-chemistry programs produce and use large amounts of data, which are usually stored on disk in the form of binary files. A FORTRAN library, named Q5Cost, has been designed and implemented in order to allow the storage of these data sets in a special data format built with the HDF5 technology. This dat...

journal_title：Journal of chemical information and modeling

authors： Borini S,Monari A,Rossi E,Tajti A,Angeli C,Bendazzoli GL,Cimiraglia R,Emerson A,Evangelisti S,Maynau D,Sanchez-Marin J,Szalay PG

更新日期：2007-05-01 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

authors： Mandal A,Johnson K,Wu CF,Bornemeier D

更新日期：2007-05-01 00:00:00

abstract：:Selecting a small subset of descriptors from a large pool to build a predictive quantitative structure-activity relationship (QSAR) model is an important step in the QSAR modeling process. In general, subset selection is very hard to solve, even approximately, with guaranteed performance bounds. Traditional approaches...

journal_title：Journal of chemical information and modeling

authors： Dutta D,Guha R,Wild D,Chen T

更新日期：2007-05-01 00:00:00

abstract：:The binding affinity and relative maximal efficacy of human A3 adenosine receptor (AR) agonists were each subjected to ligand-based three-dimensional quantitative structure-activity relationship analysis. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) used a...

journal_title：Journal of chemical information and modeling

authors： Kimand SK,Jacobson KA

更新日期：2007-05-01 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

authors： Kang H,Choi H,Park H

更新日期：2007-03-01 00:00:00

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

authors： Fink T,Reymond JL

更新日期：2007-03-01 00:00:00

abstract：:We implemented a fragment-based de novo design algorithm for a population-based optimization of molecular structures. The concept is grounded on an evolution strategy with mutation and crossover operators for structure breeding. Molecular building blocks were obtained from the pseudo-retrosynthesis of a collection of ...

journal_title：Journal of chemical information and modeling

authors： Fechner U,Schneider G

更新日期：2007-03-01 00:00:00

abstract：:Predictive metabolism methods can be used in drug discovery projects to enhance the understanding of structure-metabolism relationships. The present study uses data mining methods to exploit biotransformation data that have been recorded in the MDL Metabolite database. Reacting center fingerprints were derived from a ...

journal_title：Journal of chemical information and modeling

authors： Boyer S,Arnby CH,Carlsson L,Smith J,Stein V,Glen RC

更新日期：2007-03-01 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

authors： Agrafiotis DK,Bandyopadhyay D,Farnum M

更新日期：2007-01-01 00:00:00

abstract：:Random Forest regression (RF), Partial-Least-Squares (PLS) regression, Support Vector Machines (SVM), and Artificial Neural Networks (ANN) were used to develop QSPR models for the prediction of aqueous solubility, based on experimental data for 988 organic molecules. The Random Forest regression model predicted aqueou...

journal_title：Journal of chemical information and modeling

authors： Palmer DS,O'Boyle NM,Glen RC,Mitchell JB

更新日期：2007-01-01 00:00:00

abstract：:A major concern of chemogenomics is to associate drug activity with biological variables. Several reports have clustered cell line drug activity profiles as well as drug activity-gene expression correlation profiles and noted that the resulting groupings differ but still reflect mechanism of action. The present paper ...

journal_title：Journal of chemical information and modeling

authors： Andersson CR,Fryknäs M,Rickardson L,Larsson R,Isaksson A,Gustafsson MG

更新日期：2007-01-01 00:00:00

abstract：:Physicochemical atomic stereodescriptors (PAS) were implemented that represent the chirality of an atomic chiral center on the basis of empirical physicochemical properties of the ligands. The ligands are ranked according to a specific property, and the chiral center takes an S/R-like descriptor relative to that prope...

journal_title：Journal of chemical information and modeling

authors： Zhang QY,Aires-de-Sousa J

更新日期：2006-11-01 00:00:00

abstract：:Representative molecules from 10 classes of prohibited substances were taken from the World Anti-Doping Agency (WADA) list, augmented by molecules from corresponding activity classes found in the MDDR database. Together with some explicitly allowed compounds, these formed a set of 5245 molecules. Five types of fingerp...

journal_title：Journal of chemical information and modeling

authors： Cannon EO,Bender A,Palmer DS,Mitchell JB

更新日期：2006-11-01 00:00:00

abstract：:The configuring of a radial basis function network (RBFN) consists of selecting the network parameters (centers and widths in RBF units and weights between the hidden and output layers) and network architecture. The issues of suboptimum and overfitting, however, often occur in RBFN configuring. This paper presented a ...

journal_title：Journal of chemical information and modeling

authors： Zhou YP,Jiang JH,Lin WQ,Zou HY,Wu HL,Shen GL,Yu RQ

更新日期：2006-11-01 00:00:00

abstract：:In the present work, the Henderson-Hasselbalch (HH) equation has been employed for the development of a tool for the prediction of pH-dependent aqueous solubility of drugs and drug candidates. A new prediction method for the intrinsic solubility was developed, based on artificial neural networks that have been trained...

journal_title：Journal of chemical information and modeling

authors： Hansen NT,Kouskoumvekaki I,Jørgensen FS,Brunak S,Jónsdóttir SO

更新日期：2006-11-01 00:00:00

abstract：:Cytochrome P450 2D6 (CYP2D6) is used to develop an approach for predicting affinity and relevant binding conformation(s) for highly flexible binding sites. The approach combines the use of docking scores and compound properties as attributes in building a neural network (NN) model. It begins by identifying segments of...

journal_title：Journal of chemical information and modeling

authors： Bazeley PS,Prithivi S,Struble CA,Povinelli RJ,Sem DS

更新日期：2006-11-01 00:00:00

abstract：:The similarity/diversity measures play a fundamental role in library searching, virtual screening, and quantitative structure-activity relationship/quantitative structure-property relationship modeling as well as in genomics and proteomics. In this paper, a new similarity/diversity measure is proposed as a new approac...

journal_title：Journal of chemical information and modeling

authors： Todeschini R,Consonni V,Mauri A,Ballabio D

更新日期：2006-09-01 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

authors： Chen Q,Higgs RE,Vieth M

更新日期：2006-09-01 00:00:00

abstract：:Cathepsin A is a mammalian lysosomal enzyme that catalyzes the hydrolysis of the carboxy-terminal amino acids of polypeptides and also regulates beta-galactosidase and neuraminidase-1 activities through the formation of a multienzymic complex in lysosomes. Human cathepsin A (hCathA), yeast carboxypeptidase (CPY), and ...

journal_title：Journal of chemical information and modeling

authors： Yoshida T,Lepp Z,Kadota Y,Satoh Y,Itoh K,Chuman H

更新日期：2006-09-01 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

authors： Fitzgerald SH,Sabat M,Geysen HM

更新日期：2006-07-01 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

authors： Remko M,von der Lieth CW

更新日期：2006-07-01 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

authors： Sai Ram KV,Rambabu G,Sarma JA,Desiraju GR

更新日期：2006-07-01 00:00:00

abstract：:The Common Instrument Middleware Architecture (CIMA) aims at Grid-enabling a wide range of scientific instruments and sensors to enable easy access to and sharing and storage of data produced by these instruments and sensors. This paper describes the implementation of CIMA applied to the field of single-crystal X-ray ...

journal_title：Journal of chemical information and modeling

authors： Bramley R,Chiu K,Devadithya T,Gupta N,Hart C,Huffman JC,Huffman K,Ma Y,McMullen DF

更新日期：2006-05-01 00:00:00

abstract：:How well do different classification methods perform in selecting the ligands of a protein target out of large compound collections not used to train the model? Support vector machines, random forest, artificial neural networks, k-nearest-neighbor classification with genetic-algorithm-optimized feature selection, tren...

journal_title：Journal of chemical information and modeling

authors： Plewczynski D,Spieser SA,Koch U

更新日期：2006-05-01 00:00:00

abstract：:Molecular fingerprints are widely used for similarity-based virtual screening in drug discovery projects. In this paper we discuss the performance and the complementarity of nine two-dimensional fingerprints (Daylight, Unity, AlFi, Hologram, CATS, TRUST, Molprint 2D, ChemGPS, and ALOGP) in retrieving active molecules ...

journal_title：Journal of chemical information and modeling

authors： Kogej T,Engkvist O,Blomberg N,Muresan S

更新日期：2006-05-01 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

authors： Doddareddy MR,Cho YS,Koh HY,Kim DH,Pae AN

更新日期：2006-05-01 00:00:00

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 spat...

journal_title：Journal of chemical information and modeling

authors： Serneels S,De Nolf E,Van Espen PJ

更新日期：2006-05-01 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

authors： Gilis D

更新日期：2006-05-01 00:00:00

abstract：:Following the theoretical model by Hann et al. moderately complex structures are preferable lead compounds since they lead to specific binding events involving the complete ligand molecule. To make this concept usable in practice for library design, we studied several complexity measures on the biological activity of ...

journal_title：Journal of chemical information and modeling

authors： Schuffenhauer A,Brown N,Selzer P,Ertl P,Jacoby E

更新日期：2006-03-01 00:00:00

abstract：:This paper presents an exploratory study of a novel method for flexible 3-D similarity searching based on autocorrelation vectors and smoothed bounded distance matrices. Although the new approach is unable to outperform an existing 2-D similarity searching in terms of enrichment factors, it is able to retrieve differe...

journal_title：Journal of chemical information and modeling

authors： Rhodes N,Clark DE,Willett P

更新日期：2006-03-01 00:00:00

abstract：:It is demonstrated that the fragmentation of druglike molecules by applying simplistic pseudo-retrosynthesis results in a stock of chemically meaningful building blocks for de novo molecule generation. A stochastic search algorithm in conjunction with ligand-based similarity scoring (Flux: fragment-based ligand builde...

journal_title：Journal of chemical information and modeling

authors： Fechner U,Schneider G

更新日期：2006-03-01 00:00:00

abstract：:While critically reviewing the current status of what is known about C28H14 and C30H14 benzenoid isomers, which are ubiquitous pyrolytic constituents, some new insights will be presented. Representative isomers belonging to these benzenoid hydrocarbons are at the crossroads to homologous series that extend to infinite...

journal_title：Journal of chemical information and modeling

authors： Dias JR

更新日期：2006-03-01 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

authors： Gilis D,Biot C,Buisine E,Dehouck Y,Rooman M

更新日期：2006-03-01 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

authors： Randić M,Balaban AT

更新日期：2006-01-01 00:00:00

abstract：:The modeling of nonlinear descriptor-target relationships is a topic of considerable interest in drug discovery. We, herein, continue reporting the use of the self-organizing map-a nonlinear, topology-preserving pattern recognition technique that exhibits considerable promise in modeling and decoding these relationshi...

journal_title：Journal of chemical information and modeling

authors： Xiao YD,Harris R,Bayram E,Ii PS,Schmitt JD

更新日期：2006-01-01 00:00:00

abstract：:We demonstrate that using an all-atom molecular mechanics force field combined with an implicit solvent model for scoring protein-ligand complexes is a promising approach for improving inhibitor enrichment in the virtual screening of large compound databases. The rescoring method is evaluated by the extent to which kn...

journal_title：Journal of chemical information and modeling

authors： Huang N,Kalyanaraman C,Irwin JJ,Jacobson MP

更新日期：2006-01-01 00:00:00

abstract：:The possibility of improving the predictive ability of comparative molecular field analysis (CoMFA) by settings optimization has been evaluated to show that CoMFA predictive ability can be improved. Ten different CoMFA settings are evaluated, producing a total of 6120 models. This method has been applied to nine diffe...

journal_title：Journal of chemical information and modeling

authors： Peterson SD,Schaal W,Karlén A

更新日期：2006-01-01 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

authors： Andjus PR,Bajić A,Zhu L,Strata P

更新日期：2005-11-01 00:00:00