Molecular Dynamics Simulations of Substrate Release from Trypanosoma cruzi UDP-Galactopyranose Mutase.

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

authors： Setny P,Trylska J

更新日期：2009-02-01 00:00:00

abstract：:Generalization of an earlier algorithm has led to the development of new local structural alignment algorithms for prediction of protein-protein binding sites. The algorithms use maximum cliques on protein graphs to define structurally similar protein regions. The search for structural neighbors in the new algorithms ...

journal_title：Journal of chemical information and modeling

authors： Carl N,Konc J,Vehar B,Janezic D

更新日期：2010-10-25 00:00:00

abstract：:Partial covalent interactions (PCIs) in proteins, which include hydrogen bonds, salt bridges, cation-π, and π-π interactions, contribute to thermodynamic stability and facilitate interactions with other biomolecules. Several score functions have been developed within the Rosetta protein modeling framework that identif...

journal_title：Journal of chemical information and modeling

authors： Combs SA,Mueller BK,Meiler J

更新日期：2018-05-29 00:00:00

abstract：:G-protein-coupled receptors (GPCRs) transmit signals into the cell in response to ligand binding at its extracellular domain, which is characterized by the coupling of agonist-induced receptor conformational change to guanine nucleotide (GDP) exchange with guanosine triphosphate on a heterotrimeric (αβγ) guanine nucle...

journal_title：Journal of chemical information and modeling

authors： Kumar V,Hoag H,Sader S,Scorese N,Liu H,Wu C

更新日期：2020-08-24 00:00:00

abstract：:Advances in the development of high-throughput screening and automated chemistry have rapidly accelerated the production of chemical and biological data, much of them freely accessible through literature aggregator services such as ChEMBL and PubChem. Here, we explore how to use this comprehensive mapping of chemical ...

journal_title：Journal of chemical information and modeling

authors： Zakharov AV,Zhao T,Nguyen DT,Peryea T,Sheils T,Yasgar A,Huang R,Southall N,Simeonov A

更新日期：2019-11-25 00:00:00

abstract：:Our recent studies show that the single Tyr residue in the sequence of amyloid-β42 (Aβ42) is reactive toward various ligands, including metals and adenosine trisphospate (see: Coskuner , O. J. Biol. Inorg. Chem. 2016 , 21 , 957 - 973 and Coskuner , O. ; Murray , I. V. J. J. Alzheimer's Dis. 2014 , 41 , 561 - 574 ). Ho...

journal_title：Journal of chemical information and modeling

authors： Coskuner O,Uversky VN

更新日期：2017-06-26 00:00:00

abstract：:Resistance remains a major issue with regards to HIV-1 protease, despite the availability of numerous HIV-1 protease inhibitors and copious amounts of structural and binding data. In an effort to improve our understanding of how HIV-1 protease is able to "outsmart" new drugs, we have investigated the flexibility of HI...

journal_title：Journal of chemical information and modeling

authors： Oehme DP,Wilson DJ,Brownlee RT

更新日期：2011-05-23 00:00:00

abstract：:A comprehensive data set of aligned ligands with highly similar binding pockets from the Protein Data Bank has been built. Based on this data set, a scoring function for recognizing good alignment poses for small molecules has been developed. This function is based on atoms and hydrogen-bond projected features. The co...

journal_title：Journal of chemical information and modeling

authors： Chan SL,Labute P

更新日期：2010-09-27 00:00:00

abstract：:SMIfp (SMILES fingerprint) is defined here as a scalar fingerprint describing organic molecules by counting the occurrences of 34 different symbols in their SMILES strings, which creates a 34-dimensional chemical space. Ligand-based virtual screening using the city-block distance CBD(SMIfp) as similarity measure provi...

journal_title：Journal of chemical information and modeling

authors： Schwartz J,Awale M,Reymond JL

更新日期：2013-08-26 00:00:00

abstract：:A phenotypic screen (PS) is used to identify compounds causing a desired phenotype in a complex biological system where mechanisms and targets are largely unknown. Deconvoluting the mechanism of action of actives and identification of relevant targets and pathways remains a formidable challenge. Current methods fail t...

journal_title：Journal of chemical information and modeling

authors： Polyakov VR,Moorcroft ND,Drawid A

更新日期：2014-02-24 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：:Saturated acyclic alkanes show steric strain if they are highly branched and, in extreme cases, fall apart rapidly at room temperature. Consequently, attempts to count the number of isomeric forms for a given molecular formula that neglect this physical consideration will inevitably overestimate the size of the availa...

journal_title：Journal of chemical information and modeling

authors： Paton RS,Goodman JM

更新日期：2007-11-01 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：: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：: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：:Nonalcoholic hepatic steatosis is a worldwide epidemiological concern since it is among the most prominent hepatic diseases. Indeed, research in toxicology and epidemiology has gathered evidence that exposure to endocrine disruptors can perturb cellular homeostasis and cause this disease. Therefore, assessing the like...

journal_title：Journal of chemical information and modeling

authors： Gadaleta D,Manganelli S,Roncaglioni A,Toma C,Benfenati E,Mombelli E

更新日期：2018-08-27 00:00:00

abstract：:The chronic toxicity is fundamental for toxicological risk assessment, but its correlation with the chemical structures has been studied only little. This is partly due to the complexity of such an experimental test that embraces a plethora of different biological effects and mechanisms of action, making (Q)SAR studie...

journal_title：Journal of chemical information and modeling

authors： Mazzatorta P,Estevez MD,Coulet M,Schilter B

更新日期：2008-10-01 00:00:00

abstract：:In this work, the perception of similarity of reactions catalyzed by hydrolases and oxidoreductases on the basis of the overall breaking and making of bonds of reactions is investigated. Six physicochemical properties for the reacting bond in the substrate of each enzymatic reaction were calculated to describe the cha...

journal_title：Journal of chemical information and modeling

authors： Hu X,Yan A,Tan T,Sacher O,Gasteiger J

更新日期：2010-06-28 00:00:00

abstract：:Big data is one of the key transformative factors which increasingly influences all aspects of modern life. Although this transformation brings vast opportunities it also generates novel challenges, not the least of which is organizing and searching this data deluge. The field of medicinal chemistry is not different: ...

journal_title：Journal of chemical information and modeling

authors： Schneider N,Fechner N,Landrum GA,Stiefl N

更新日期：2017-08-28 00:00:00

abstract：:With continually increased computer power, molecular mechanics force field-based approaches, such as the endpoint methods of molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics generalized Born surface area (MM-GBSA), have been routinely applied in both drug lead identification and opt...

journal_title：Journal of chemical information and modeling

authors： Hao D,He X,Ji B,Zhang S,Wang J

更新日期：2020-12-28 00:00:00

abstract：:A new web portal for the CHARMM macromolecular modeling package, CHARMMing (CHARMM interface and graphics, http://www.charmming.org), is presented. This tool provides a user-friendly interface for the preparation, submission, monitoring, and visualization of molecular simulations (i.e., energy minimization, solvation,...

journal_title：Journal of chemical information and modeling

authors： Miller BT,Singh RP,Klauda JB,Hodoscek M,Brooks BR,Woodcock HL 3rd

更新日期：2008-09-01 00:00:00

abstract：:The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In th...

journal_title：Journal of chemical information and modeling

authors： Won J,Lee GR,Park H,Seok C

更新日期：2018-06-25 00:00:00

abstract：:With chemical libraries increasingly containing millions of compounds or more, there is a fast-growing need for computational methods that can rank or prioritize compounds for screening. Machine learning methods have shown considerable promise for this task; indeed, classification methods such as support vector machin...

journal_title：Journal of chemical information and modeling

authors： Agarwal S,Dugar D,Sengupta S

更新日期：2010-05-24 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：:We present an algorithm, ReFlex3D, for the refinement of flexible molecular alignments based on their three-dimensional shape and electrostatic properties. The algorithm is designed to be used with fast conformer generators to refine an initial overlay between two molecules and thus to obtain improved overlaps as judg...

journal_title：Journal of chemical information and modeling

authors： Schmidt TC,Cosgrove DA,Boström J

更新日期：2018-04-23 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：:To discover non-nucleoside inhibitors of HIV-1 reverse transcriptase (NNRTIs) that are effective against both wild-type (WT) virus and variants that encode the clinically troublesome Tyr181Cys (Y181C) RT mutation, virtual screening by docking was carried out using three RT structures and more than 2 million commercial...

journal_title：Journal of chemical information and modeling

authors： Nichols SE,Domaoal RA,Thakur VV,Tirado-Rives J,Anderson KS,Jorgensen WL

更新日期：2009-05-01 00:00:00

abstract：:Fast and accurate predicting of the binding affinities of large sets of diverse protein−ligand complexes is an important, yet extremely challenging, task in drug discovery. The development of knowledge-based scoring functions exploiting structural information of known protein−ligand complexes represents a valuable con...

journal_title：Journal of chemical information and modeling

authors： Shen Q,Xiong B,Zheng M,Luo X,Luo C,Liu X,Du Y,Li J,Zhu W,Shen J,Jiang H

更新日期：2011-02-28 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：:Universal generative topographic maps (GTMs) provide two-dimensional representations of chemical space selected for their "polypharmacological competence", that is, the ability to simultaneously represent meaningful activity and property landscapes, associated with many distinct targets and properties. Several such GT...

journal_title：Journal of chemical information and modeling

authors： Casciuc I,Zabolotna Y,Horvath D,Marcou G,Bajorath J,Varnek A

更新日期：2019-01-28 00:00:00