abstract：:Finding a canonical ordering of the atoms in a molecule is a prerequisite for generating a unique representation of the molecule. The canonicalization of a molecule is usually accomplished by applying some sort of graph relaxation algorithm, the most common of which is the Morgan algorithm. There are known issues with...

journal_title：Journal of chemical information and modeling

authors： Schneider N,Sayle RA,Landrum GA

更新日期：2015-10-26 00:00:00

abstract：:The industrial production of higher-generation semisynthetic cephalosporins starts from 7-aminocephalosporanic acid (7-ACA), which is obtained by deacylation of the naturally occurring antibiotic cephalosporin C (CephC). The enzymatic process in which CephC is directly converted into 7-ACA by a cephalosporin C acylase...

journal_title：Journal of chemical information and modeling

authors： Mollica L,Conti G,Pollegioni L,Cavalli A,Rosini E

更新日期：2015-10-26 00:00:00

abstract：:With the hope of discovering effective analgesics with fewer side effects, attention has recently shifted to allosteric modulators of the opioid receptors. In the past two years, the first chemotypes of positive or silent allosteric modulators (PAMs or SAMs, respectively) of μ- and δ-opioid receptor types have been re...

journal_title：Journal of chemical information and modeling

authors： Bisignano P,Burford NT,Shang Y,Marlow B,Livingston KE,Fenton AM,Rockwell K,Budenholzer L,Traynor JR,Gerritz SW,Alt A,Filizola M

更新日期：2015-09-28 00:00:00

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

authors： Galat A

更新日期：2015-09-28 00:00:00

abstract：:The in silico prediction of unwanted side effects (SEs) caused by the promiscuous behavior of drugs and their targets is highly relevant to the pharmaceutical industry. Considerable effort is now being put into computational and experimental screening of several suspected off-target proteins in the hope that SEs might...

journal_title：Journal of chemical information and modeling

authors： Pérez-Nueno VI,Souchet M,Karaboga AS,Ritchie DW

更新日期：2015-09-28 00:00:00

abstract：:Inhibition of protein-protein interactions (PPIs) is emerging as a promising therapeutic strategy despite the difficulty in targeting such interfaces with drug-like small molecules. PPIs generally feature large and flat binding surfaces as compared to typical drug targets. These features pose a challenge for structura...

journal_title：Journal of chemical information and modeling

authors： Rooklin D,Wang C,Katigbak J,Arora PS,Zhang Y

更新日期：2015-08-24 00:00:00

abstract：:The SZMAP method computes binding free energies and the corresponding thermodynamic components for water molecules in the binding site of a protein structure [ SZMAP, 1.0.0 ; OpenEye Scientific Software Inc. : Santa Fe, NM, USA , 2011 ]. In this work, the ability of SZMAP to predict water structure and thermodynamic s...

journal_title：Journal of chemical information and modeling

authors： Bayden AS,Moustakas DT,Joseph-McCarthy D,Lamb ML

更新日期：2015-08-24 00:00:00

abstract：:Porcupine is a component of the Wnt pathway which regulates cell proliferation, migration, stem cell self-renewal, and differentiation. The Wnt pathway has been shown to be dysregulated in a variety of cancers. Porcupine is a membrane bound O-acyltransferase that palmitoylates Wnt. Inhibiting porcupine blocks the secr...

journal_title：Journal of chemical information and modeling

authors： Poulsen A,Ho SY,Wang W,Alam J,Jeyaraj DA,Ang SH,Tan ES,Lin GR,Cheong VW,Ke Z,Lee MA,Keller TH

更新日期：2015-07-27 00:00:00

abstract：:A comprehensive safety evaluation of chemicals should require toxicity assessment in both the aquatic and terrestrial test species. Due to the application practices and nature of chemical pesticides, the avian toxicity testing is considered as an essential requirement in the risk assessment process. In this study, tre...

journal_title：Journal of chemical information and modeling

authors： Basant N,Gupta S,Singh KP

更新日期：2015-07-27 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

authors： Gaudreault F,Najmanovich RJ

更新日期：2015-07-27 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

authors： Clark AM,Dole K,Coulon-Spektor A,McNutt A,Grass G,Freundlich JS,Reynolds RC,Ekins S

更新日期：2015-06-22 00:00:00

abstract：:Nonfibrillar neurotoxic amyloid β (Aβ) oligomer structures are typically rich in β-sheets, which could be promoted by metal ions like Zn(2+). Here, using molecular dynamics (MD) simulations, we systematically examined combinations of Aβ40 peptide conformations and Zn(2+) binding modes to probe the effects of secondary...

journal_title：Journal of chemical information and modeling

authors： Xu L,Shan S,Chen Y,Wang X,Nussinov R,Ma B

更新日期：2015-06-22 00:00:00

abstract：:The ongoing search for fast Li-ion conducting solid electrolytes has driven the deployment surge on density functional theory (DFT) computation and materials informatics for exploring novel chemistries before actual experimental testing. Existing structure prototypes can now be readily evaluated beforehand not only to...

journal_title：Journal of chemical information and modeling

authors： Jalem R,Kimura M,Nakayama M,Kasuga T

更新日期：2015-06-22 00:00:00

abstract：:Due to the importance of hot-spots (HS) detection and the efficiency of computational methodologies, several HS detecting approaches have been developed. The current paper presents new models to predict HS for protein-protein and protein-nucleic acid interactions with better statistics compared with the ones currently...

journal_title：Journal of chemical information and modeling

authors： Munteanu CR,Pimenta AC,Fernandez-Lozano C,Melo A,Cordeiro MN,Moreira IS

更新日期：2015-05-26 00:00:00

abstract：:Molecular fragment dynamics (MFD) is a variant of dissipative particle dynamics (DPD), a coarse-grained mesoscopic simulation technique for isothermal complex fuids and soft matter systems with particles that are chosen to be adequate fluid elements. MFD choses its particles to be small molecules which may be connecte...

journal_title：Journal of chemical information and modeling

authors： Truszkowski A,van den Broek K,Kuhn H,Zielesny A,Epple M

更新日期：2015-05-26 00:00:00

abstract：:HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X...

journal_title：Journal of chemical information and modeling

authors： Riccardi D,Parks JM,Johs A,Smith JC

更新日期：2015-04-27 00:00:00

abstract：:LEAFY (LFY) is a plant-specific transcription factor, with a variety of roles in different species. LFY contains a conserved DNA-binding domain (DBD) that determines its DNA-binding specificity. Recently, the structures of the dimeric LFY-DBD bound to different DNA motifs were successively solved by X-ray crystallogra...

journal_title：Journal of chemical information and modeling

authors： Wan H,Chang S,Hu JP,Tian YX,Tian XH

更新日期：2015-04-27 00:00:00

abstract：:Histone deacetylases (HDACs) are an important class of drug targets for the treatment of cancers, neurodegenerative diseases, and other types of diseases. Virtual screening (VS) has become fairly effective approaches for drug discovery of novel and highly selective histone deacetylase inhibitors (HDACIs). To facilitat...

journal_title：Journal of chemical information and modeling

authors： Xia J,Tilahun EL,Kebede EH,Reid TE,Zhang L,Wang XS

更新日期：2015-02-23 00:00:00

abstract：:A generic chemical transformation may often be achieved under various synthetic conditions. However, for any specific reagents, only one or a few among the reported synthetic protocols may be successful. For example, Michael β-addition reactions may proceed under different choices of solvent (e.g., hydrophobic, aproti...

journal_title：Journal of chemical information and modeling

authors： Marcou G,Aires de Sousa J,Latino DA,de Luca A,Horvath D,Rietsch V,Varnek A

更新日期：2015-02-23 00:00:00

abstract：:Maltose-binding protein is a periplasmic binding protein responsible for transport of maltooligosaccarides through the periplasmic space of Gram-negative bacteria, as a part of the ABC transport system. The molecular mechanisms of the initial ligand binding and induced large scale motion of the protein's domains still...

journal_title：Journal of chemical information and modeling

authors： Huang W,Blinov N,Wishart DS,Kovalenko A

更新日期：2015-02-23 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

authors： Oliveira TB,Gobbo-Neto L,Schmidt TJ,Da Costa FB

更新日期：2015-01-26 00:00:00

abstract：:Determination of structural similarities between protein binding pockets is an important challenge in in silico drug design. It can help to understand selectivity considerations, predict unexpected ligand cross-reactivity, and support the putative annotation of function to orphan proteins. To this end, Cavbase was dev...

journal_title：Journal of chemical information and modeling

authors： Krotzky T,Grunwald C,Egerland U,Klebe G

更新日期：2015-01-26 00:00:00

abstract：:Growing data sets with increased time for analysis is hampering predictive modeling in drug discovery. Model building can be carried out on high-performance computer clusters, but these can be expensive to purchase and maintain. We have evaluated ligand-based modeling on cloud computing resources where computations ar...

journal_title：Journal of chemical information and modeling

authors： Moghadam BT,Alvarsson J,Holm M,Eklund M,Carlsson L,Spjuth O

更新日期：2015-01-26 00:00:00

abstract：:Sterol 14α-demethylase (CYP51) is the main drug target for the treatment of fungal infections. The discovery of new efficient fungal CYP51 inhibitors requires an understanding of the structural requirements for selectivity for the fungal over the human ortholog. In this study, a binding mode of the pyridylethanol(phen...

journal_title：Journal of chemical information and modeling

authors： Zelenko U,Hodošček M,Rozman D,Golič Grdadolnik S

更新日期：2014-12-22 00:00:00

abstract：:A compound's synthetic accessibility (SA) is an important aspect of drug design, since in some cases computer-designed compounds cannot be synthesized. There have been several reports on SA prediction, most of which have focused on the difficulties of synthetic reactions based on retro-synthesis analyses, reaction dat...

journal_title：Journal of chemical information and modeling

authors： Fukunishi Y,Kurosawa T,Mikami Y,Nakamura H

更新日期：2014-12-22 00:00:00

abstract：:We report a new classification method for pyranose ring conformations called Best-fit, Four-Membered Plane (BFMP), which describes pyranose ring conformations based on reference planes defined by four atoms. The method is able to characterize all asymmetrical and symmetrical shapes of a pyran ring, is readily automate...

journal_title：Journal of chemical information and modeling

authors： Makeneni S,Foley BL,Woods RJ

更新日期：2014-10-27 00:00:00

abstract：:The yeast protein GCN4 is a transcriptional activator in the basic leucine zipper (bZip) family, whose distinguishing feature is the "chopstick-like" homodimer of alpha helices formed at the DNA-binding interface. While experiments have shown that truncated versions of the protein retain biologically relevant DNA-bind...

journal_title：Journal of chemical information and modeling

authors： McHarris DM,Barr DA

更新日期：2014-10-27 00:00:00

abstract：:Naturally occurring anticancer compounds represent about half of the chemotherapeutic drugs which have been put in the market against cancer until date. Computer-based or in silico virtual screening methods are often used in lead/hit discovery protocols. In this study, the "drug-likeness" of ~400 compounds from Africa...

journal_title：Journal of chemical information and modeling

authors： Ntie-Kang F,Nwodo JN,Ibezim A,Simoben CV,Karaman B,Ngwa VF,Sippl W,Adikwu MU,Mbaze LM

更新日期：2014-09-22 00:00:00

abstract：:Accurate and affordable assessment of ligand-protein affinity for structure-based virtual screening (SB-VS) is a standing challenge. Hence, empirical postdocking filters making use of various types of structure-activity information may prove useful. Here, we introduce one such filter based upon three-dimensional struc...

journal_title：Journal of chemical information and modeling

authors： Da C,Kireev D

更新日期：2014-09-22 00:00:00

abstract：:The accurate prediction of the adsorption energies of unsaturated molecules on graphene in the presence of water is essential for the design of molecules that can modify its properties and that can aid its processability. We here show that a semiempirical MO method corrected for dispersive interactions (PM6-DH2) can p...

journal_title：Journal of chemical information and modeling

authors： Vincent MA,Hillier IH

更新日期：2014-08-25 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

authors： Avram SI,Pacureanu LM,Bora A,Crisan L,Avram S,Kurunczi L

更新日期：2014-08-25 00:00:00

abstract：:Physicochemical properties of compounds have been instrumental in selecting lead compounds with increased drug-likeness. However, the relationship between physicochemical properties of constituent drugs and the tendency to exhibit drug interaction has not been systematically studied. We assembled physicochemical descr...

journal_title：Journal of chemical information and modeling

authors： Yilancioglu K,Weinstein ZB,Meydan C,Akhmetov A,Toprak I,Durmaz A,Iossifov I,Kazan H,Roth FP,Cokol M

更新日期：2014-08-25 00:00:00

abstract：:Structure-based computational target prediction methods identify potential targets for a bioactive compound. Methods based on protein-ligand docking so far face many challenges, where the greatest probably is the ranking of true targets in a large data set of protein structures. Currently, no standard data sets for ev...

journal_title：Journal of chemical information and modeling

authors： Schomburg KT,Rarey M

更新日期：2014-08-25 00:00:00

abstract：:Protein-protein interactions play a key role in a multitude of biological processes, such as signal transduction, de novo drug design, immune responses, and enzymatic activities. It is of great interest to understand how proteins interact with each other. The general approach is to explore all possible poses and ident...

journal_title：Journal of chemical information and modeling

authors： Guo F,Li SC,Du P,Wang L

更新日期：2014-06-23 00:00:00

abstract：:Homology modeling is a reliable method of predicting the three-dimensional structures of proteins that lack NMR or X-ray crystallographic data. It employs the assumption that a structural resemblance exists between closely related proteins. Despite the availability of many crystal structures of possible templates, onl...

journal_title：Journal of chemical information and modeling

authors： Rataj K,Witek J,Mordalski S,Kosciolek T,Bojarski AJ

更新日期：2014-06-23 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

authors： Carrió P,Pinto M,Ecker G,Sanz F,Pastor M

更新日期：2014-05-27 00:00:00

abstract：:In this study we investigate π-stacking interactions of a variety of aromatic heterocycles with benzene using dispersion corrected density functional theory. We calculate extensive potential energy surfaces for parallel-displaced interaction geometries. We find that dispersion contributes significantly to the interact...

journal_title：Journal of chemical information and modeling

authors： Huber RG,Margreiter MA,Fuchs JE,von Grafenstein S,Tautermann CS,Liedl KR,Fox T

更新日期：2014-05-27 00:00:00

abstract：:The emergence of multidrug-resistant Staphylococcus aureus (S. aureus) makes the treatment of infectious diseases in hospitals more difficult and increases the mortality of the patients. In this study, we attempted to identify novel potent antibiotic candidate compounds against S. aureus dihydrofolate reductase (saDHF...

journal_title：Journal of chemical information and modeling

authors： Kobayashi M,Kinjo T,Koseki Y,Bourne CR,Barrow WW,Aoki S

更新日期：2014-04-28 00:00:00

abstract：:The consistent handling of molecules is probably the most basic and important requirement in the field of cheminformatics. Reliable results can only be obtained if the underlying calculations are independent of the specific way molecules are represented in the input data. However, ensuring consistency is a complex tas...

journal_title：Journal of chemical information and modeling

authors： Urbaczek S,Kolodzik A,Rarey M

更新日期：2014-03-24 00:00:00

abstract：:This work is aimed at describing the workflow for a methodology that combines chemoinformatics and pharmacoepidemiology methods and at reporting the first predictive model developed with this methodology. The new model is able to predict complex networks of AIDS prevalence in the US counties, taking into consideration...

journal_title：Journal of chemical information and modeling

authors： González-Díaz H,Herrera-Ibatá DM,Duardo-Sánchez A,Munteanu CR,Orbegozo-Medina RA,Pazos A

更新日期：2014-03-24 00:00:00