Discovery of New SIRT2 Inhibitors by Utilizing a Consensus Docking/Scoring Strategy and Structure-Activity Relationship Analysis.

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：:The enzyme UDP-galactopyranose mutase (UGM) represents a promising drug target for the treatment of infections with Trypanosoma cruzi. We have computed the Potential of Mean Force for the release of UDP-galactopyranose from UGM, using Umbrella Sampling simulations. The simulations revealed the conformational changes t...

journal_title：Journal of chemical information and modeling

authors： Cossio-Pérez R,Pierdominici-Sottile G,Sobrado P,Palma J

更新日期：2019-02-25 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：:The important role of water molecules in protein-ligand binding energetics has attracted wide attention in recent years. A range of computational methods has been developed to predict the favorable locations of water molecules in a protein binding pocket. Most of the current methods are based on extensive molecular dy...

journal_title：Journal of chemical information and modeling

authors： Li Y,Gao Y,Holloway MK,Wang R

更新日期：2020-09-28 00:00:00

abstract：:Class II fructose-1,6-bisphosphate aldolases (FBA-II) are attractive new targets for the discovery of drugs to combat invasive fungal infection, because they are absent in animals and higher plants. Although several FBA-II inhibitors have been reported, none of these inhibitors exhibit antifungal effect so far. In thi...

journal_title：Journal of chemical information and modeling

authors： Han X,Zhu X,Hong Z,Wei L,Ren Y,Wan F,Zhu S,Peng H,Guo L,Rao L,Feng L,Wan J

更新日期：2017-06-26 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：:Traditionally, a drug potency is expressed in terms of thermodynamic quantities, mostly Kd, and empirical IC50 values. Although binding affinity as an estimate of drug activity remains relevant, it is increasingly clear that it is also important to include (un)binding kinetic parameters in the characterization of pote...

journal_title：Journal of chemical information and modeling

authors： Bernetti M,Rosini E,Mollica L,Masetti M,Pollegioni L,Recanatini M,Cavalli A

更新日期：2018-11-26 00:00:00

abstract：:The metabolism of xenobiotics--and more specifically drugs--in the liver is a critical process controlling their half-life. Although there exist experimental methods, which measure the metabolic stability of xenobiotics and identify their metabolites, developing higher throughput predictive methods is an avenue of res...

journal_title：Journal of chemical information and modeling

authors： Campagna-Slater V,Pottel J,Therrien E,Cantin LD,Moitessier N

更新日期：2012-09-24 00:00:00

abstract：:A machine learning enhanced spectrum recognition system called spectrum recognition based on computer vision (SRCV) for data extraction from previously analyzed 13C and 1H NMR spectra has been developed. The intelligent system was designed with four function modules to extract data from three areas of NMR images, incl...

journal_title：Journal of chemical information and modeling

authors： Jia W,Yang Z,Yang M,Cheng L,Lei Z,Wang X

更新日期：2021-01-25 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 high-throughput docking protocol called ALTA-VS (anchor-based library tailoring approach for virtual screening) was developed in 2005 for the efficient in silico screening of large libraries of compounds by preselection of only those molecules that have optimal fragments (anchors) for the protein target. Here we p...

journal_title：Journal of chemical information and modeling

authors： Marchand JR,Dalle Vedove A,Lolli G,Caflisch A

更新日期：2017-10-23 00:00:00

abstract：:The momentum gained by research on biologics has not been met yet with equal thrust on the informatics side. There is a noticeable lack of software for data management that empowers the bench scientists working on the development of biologic therapeutics. SARvision|Biologics is a tool to analyze data associated with b...

journal_title：Journal of chemical information and modeling

authors： Hansen MR,Villar HO,Feyfant E

更新日期：2013-10-28 00:00:00

abstract：:In this work, we present molecular modeling studies carried out using six DNA sequences and six azinomycin analogues, including the naturally occurring compound azinomycin B, selected on the basis of known cell cytotoxicity and structural analogies (epoxide and aziridine alkylating moieties). Among several computation...

journal_title：Journal of chemical information and modeling

authors： Alcaro S,Ortuso F,Coleman RS

更新日期：2005-05-01 00:00:00

abstract：:The integration of ligand- and structure-based strategies might sensitively increase the success of drug discovery process. We have recently described the application of Molecular Electrostatic Potential autocorrelated vectors (autoMEPs) in generating both linear (Partial Least-Square, PLS) and nonlinear (Response Sur...

journal_title：Journal of chemical information and modeling

authors： Michielan L,Bacilieri M,Schiesaro A,Bolcato C,Pastorin G,Spalluto G,Cacciari B,Klotz KN,Kaseda C,Moro S

更新日期：2008-02-01 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：: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：: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：: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：: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

authors： Schwaighofer A,Schroeter T,Mika S,Hansen K,Ter Laak A,Lienau P,Reichel A,Heinrich N,Müller KR

更新日期：2008-04-01 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：: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：: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：: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：: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：:Curvularia lunata is a dark pigmented fungus that is the causative agent of several diseases in plants and in both immunodeficient and immunocompetent patients. 1,8-Dihydroxynaphthalene-melanin is found in the cell wall of C. lunata and is believed to be the important virulence factor of dematiaceous fungi. Trihydroxy...

journal_title：Journal of chemical information and modeling

authors： Brunskole Svegelj M,Turk S,Brus B,Lanisnik Rizner T,Stojan J,Gobec S

更新日期：2011-07-25 00:00:00

abstract：:With the emergence of large collections of protein-ligand complexes complemented by binding data, as found in PDBbind or BindingMOAD, new opportunities for parametrizing and evaluating scoring functions have arisen. With huge data collections available, it becomes feasible to fit scoring functions in a QSAR style, i.e...

journal_title：Journal of chemical information and modeling

authors： Kramer C,Gedeck P

更新日期：2010-11-22 00:00:00

abstract：:Cyanobacterial fructose-1,6-/sedoheptulose-1,7-bisphoshatase (cy-FBP/SBPase) is a potential enzymatic target for screening of novel inhibitors that can combat harmful algal blooms. In the present study, we targeted the substrate binding pocket of cy-FBP/SBPase. A series of novel hit compounds from the SPECs database w...

journal_title：Journal of chemical information and modeling

authors： Sun Y,Zhang R,Li D,Feng L,Wu D,Feng L,Huang P,Ren Y,Feng J,Xiao S,Wan J

更新日期：2014-03-24 00:00:00

abstract：:Understanding the relationship between chemical structure and function is a ubiquitous problem within the fields of chemistry and biology. Simulation approaches attack the problem utilizing physics to understand a given process at the particle level. Unfortunately, these approaches are often too expensive for many pro...

journal_title：Journal of chemical information and modeling

authors： Brown WM,Sasson A,Bellew DR,Hunsaker LA,Martin S,Leitao A,Deck LM,Vander Jagt DL,Oprea TI

更新日期：2008-08-01 00:00:00

abstract：:Deep learning methods applied to problems in chemoinformatics often require the use of recursive neural networks to handle data with graphical structure and variable size. We present a useful classification of recursive neural network approaches into two classes, the inner and outer approach. The inner approach uses r...

journal_title：Journal of chemical information and modeling

authors： Urban G,Subrahmanya N,Baldi P

更新日期：2018-02-26 00:00:00

abstract：:Support vector regression (SVR) is a premier approach for the prediction of compound potency. Given the conceptual link between support vector machine (SVM) and SVR modeling, SVR is capable of accounting for continuous and discontinuous structure-activity relationships (SARs) in potency prediction, which further exten...

journal_title：Journal of chemical information and modeling

authors： Miyao T,Funatsu K,Bajorath J

更新日期：2019-03-25 00:00:00