Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations.

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

authors： Kapaev RR,Toukach PV

更新日期：2016-06-27 00:00:00

abstract：:In this account, a rapid retrosynthesis-based scoring method for the assessment of synthetic accessibility of drug-like molecules, called RASA (Retrosynthesis-based Assessment of Synthetic Accessibility) is devised. RASA first constructs a synthesis tree for the target molecule based on retrosynthetic analysis; in thi...

journal_title：Journal of chemical information and modeling

authors： Huang Q,Li LL,Yang SY

更新日期：2011-10-24 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

authors： Ehrlich HC,Henzler AM,Rarey M

更新日期：2013-07-22 00:00:00

abstract：:Insect neuropeptide receptors, including allatostatin receptor type C (AstR-C), a G protein-coupled receptor, are among the potential targets for designing next-generation pesticides that despite their importance in offering a new mode-of-action have been overlooked. Focusing on AstR-C of Thaumetopoea pityocampa, a co...

journal_title：Journal of chemical information and modeling

authors： Shahraki A,Işbilir A,Dogan B,Lohse MJ,Durdagi S,Birgul-Iyison N

更新日期：2021-01-21 00:00:00

abstract：:Three-dimensional protein structures are a key requisite for structure-based drug discovery. For many highly relevant targets, medicinal chemists are confronted with large numbers of target structures in their apo-forms or in complex with a wealth of different ligands. To exploit the full potential of such structure e...

journal_title：Journal of chemical information and modeling

authors： Schmalhorst PS,Bergner A

更新日期：2020-04-27 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：:Proteins often have both orthosteric and allosteric binding sites. Endogenous ligands, such as hormones and neurotransmitters, bind to the orthosteric site, while synthetic ligands may bind to orthosteric or allosteric sites, which has become a focal point in drug discovery. Usually, such allosteric modulators bind to...

journal_title：Journal of chemical information and modeling

authors： Burggraaff L,van Veen A,Lam CC,van Vlijmen HWT,IJzerman AP,van Westen GJP

更新日期：2020-10-26 00:00:00

abstract：:In this work, we present a systematical investigation of the influence of ligand protonation states, stereoisomers, and tautomers on results obtained with the two protein-ligand docking programs GOLD and PLANTS. These different states were generated with a fully automated tool, called SPORES (Structure PrOtonation and...

journal_title：Journal of chemical information and modeling

authors： ten Brink T,Exner TE

更新日期：2009-06-01 00:00:00

abstract：:Binding affinity prediction with implicit solvent models remains a challenge in virtual screening for drug discovery. In order to assess the predictive power of implicit solvent models in docking techniques with Amber scoring, three generalized Born models (GBHCT, GBOBCI, and GBOBCII) available in Dock 6.7 were utiliz...

journal_title：Journal of chemical information and modeling

authors： Zhang H,Yin C,Yan H,van der Spoel D

更新日期：2016-10-24 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

authors： Guest EE,Oatley SA,Macdonald SJF,Hirst JD

更新日期：2020-11-23 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

authors： Schmidt TC,Eriksson PO,Gustafsson D,Cosgrove D,Frølund B,Boström J

更新日期：2017-07-24 00:00:00

abstract：:Protein-protein interactions (PPIs) play vital roles in regulating biological processes, such as cellular and signaling pathways. Hotspots are certain residues located at protein-protein interfaces that contribute more in protein-protein binding than other residues. Research on the mutational effects of hotspots is im...

journal_title：Journal of chemical information and modeling

authors： Wu FX,Yang JF,Mei LC,Wang F,Hao GF,Yang GF

更新日期：2021-01-25 00:00:00

abstract：:Databases of small, potentially bioactive molecules are ubiquitous across the industry and academia. Designed such that each unique compound should appear only once, the multiplicity of ways in which many compounds can be represented means that these databases require methods for standardizing the representation of ch...

journal_title：Journal of chemical information and modeling

authors： Baker CM,Kidley NJ,Papachristos K,Hotson M,Carson R,Gravestock D,Pouliot M,Harrison J,Dowling A

更新日期：2020-08-24 00:00:00

abstract：:We present a succession of structural changes involved in hormone peptide activation of a prototypical GPCR. Microsecond molecular dynamics simulation generated conformational ensembles reveal propagation of structural changes through key "microswitches" within human AT1R bound to native hormone. The endocrine octa-pe...

journal_title：Journal of chemical information and modeling

authors： Singh KD,Unal H,Desnoyer R,Karnik SS

更新日期：2019-01-28 00:00:00

abstract：:We introduce SARANEA, an open-source Java application for interactive exploration of structure-activity relationship (SAR) and structure-selectivity relationship (SSR) information in compound sets of any source. SARANEA integrates various SAR and SSR analysis functions and utilizes a network-like similarity graph data...

journal_title：Journal of chemical information and modeling

authors： Lounkine E,Wawer M,Wassermann AM,Bajorath J

更新日期：2010-01-01 00:00:00

abstract：:In this study, we tried to establish a general scheme to create a model that could predict the affinity of small compounds to their target proteins. This scheme consists of a search for ligand-binding sites on a protein, a generation of bound conformations (poses) of ligands in each of the sites by docking, identifica...

journal_title：Journal of chemical information and modeling

authors： Yasuo K,Yamaotsu N,Gouda H,Tsujishita H,Hirono S

更新日期：2009-04-01 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：:An index of the activation of Class A G-protein-coupled receptors (GPCRs) has been trained using interhelix distances from a series of microsecond molecular-dynamics simulations and tested for 268 published X-ray structures. In a three-class model that includes intermediate structures, 63% of the active structures are...

journal_title：Journal of chemical information and modeling

authors： Ibrahim P,Wifling D,Clark T

更新日期：2019-09-23 00:00:00

abstract：:Accurate hydrogen placement in molecular modeling is crucial for studying the interactions and dynamics of biomolecular systems. The carboxyl functional group is a prototypical example of a functional group that requires protonation during structure preparation. To our knowledge, when in their neutral form, carboxylic...

journal_title：Journal of chemical information and modeling

authors： Lim VT,Bayly CI,Fusti-Molnar L,Mobley DL

更新日期：2019-05-28 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：:Large corpora of kinase small molecule inhibitor data are accessible to public sector research from thousands of journal article and patent publications. These data have been generated employing a wide variety of assay methodologies and experimental procedures by numerous laboratories. Here we ask the question how app...

journal_title：Journal of chemical information and modeling

authors： Schürer SC,Muskal SM

更新日期：2013-01-28 00:00:00

abstract：:Machine learning has exhibited powerful capabilities in many areas. However, machine learning models are mostly database dependent, requiring a new model if the database changes. Therefore, a universal model is highly desired to accommodate the widest variety of databases. Fortunately, this universality may be achieve...

journal_title：Journal of chemical information and modeling

authors： Li W,Miao W,Cui J,Fang C,Su S,Li H,Hu L,Lu Y,Chen G

更新日期：2019-05-28 00:00:00

abstract：:Metabolism of xenobiotic and endogenous compounds is frequently complex, not completely elucidated, and therefore often ambiguous. The prediction of sites of metabolism (SoM) can be particularly helpful as a first step toward the identification of metabolites, a process especially relevant to drug discovery. This pape...

journal_title：Journal of chemical information and modeling

authors： Tyzack JD,Williamson MJ,Torella R,Glen RC

更新日期：2013-06-24 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

authors： Hartono YD,Xu Y,Karshikoff A,Nilsson L,Villa A

更新日期：2018-04-23 00:00:00

abstract：:The prediction of Log P is usually accomplished using either substructure or whole-molecule approaches. However, these methods are complicated, and previous whole-molecule approaches have not been successful for the prediction of Log P in very complex molecules. The observed chemical shifts in nuclear magnetic resonan...

journal_title：Journal of chemical information and modeling

authors： Schnackenberg LK,Beger RD

更新日期：2005-03-01 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

authors： Hewitt M,Cronin MT,Madden JC,Rowe PH,Johnson C,Obi A,Enoch SJ

更新日期：2007-07-01 00:00:00

abstract：:Understanding which physicochemical properties, or property distributions, are favorable for successful design and development of drugs, nutritional supplements, cosmetics, and agrochemicals is of great importance. In this study we have analyzed molecules from three distinct chemical spaces (i) approved drugs, (ii) hu...

journal_title：Journal of chemical information and modeling

authors： Kirchmair J,Howlett A,Peironcely JE,Murrell DS,Williamson MJ,Adams SE,Hankemeier T,van Buren L,Duchateau G,Klaffke W,Glen RC

更新日期：2013-02-25 00:00:00

abstract：:3-Pyridyl ethers are excellent nAChRs ligands, which show high subtype selectivity and binding affinity to alpha4beta2 nAChR. Although the quantitative structure-activity relationship (QSAR) of nAChRs ligands has been widely investigated using various classes of compounds, the open ring analogues of 3-pyridyl ethers h...

journal_title：Journal of chemical information and modeling

authors： Zhang H,Li H,Liu C

更新日期：2005-03-01 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：:DiSCuS, a "Database System for Compound Selection", has been developed. The primary goal of DiSCuS is to aid researchers in the steps subsequent to generating high-throughput virtual screening (HTVS) results, such as selection of compounds for further study, purchase, or synthesis. To do so, DiSCuS provides (1) a stor...

journal_title：Journal of chemical information and modeling

authors： Wójcikowski M,Zielenkiewicz P,Siedlecki P

更新日期：2014-01-27 00:00:00