From Brazil to Germany: Challenges and Advantages.

abstract：:The worldwide increase and proliferation of drug resistant microbes, coupled with the lag in new drug development, represents a major threat to human health. In order to reduce the time and cost for exploring the chemical search space, drug discovery increasingly relies on computational biology approaches. One key ste...

journal_title：Journal of chemical information and modeling

authors： Hassan-Harrirou H,Zhang C,Lemmin T

更新日期：2020-06-22 00:00:00

abstract：:A giant technological leap in the field of cryo-electron microscopy (cryo-EM) has assured the achievement of near-atomic resolution structures of biological macromolecules. As a recognition of this accomplishment, the Nobel Prize in Chemistry was awarded in 2017 to Jacques Dubochet, Joachim Frank, and Richard Henderso...

journal_title：Journal of chemical information and modeling

authors： Akbar S,Mozumder S,Sengupta J

更新日期：2020-05-26 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：:The causative agent of African sleeping sickness, Trypanosoma brucei , undergoes an unusual mitochondrial RNA editing process that is essential for its survival. RNA editing terminal uridylyl transferase 2 of T. brucei (TbRET2) is an indispensable component of the editosome machinery that performs this editing. TbR...

journal_title：Journal of chemical information and modeling

authors： Demir Ö,Amaro RE

更新日期：2012-05-25 00:00:00

abstract：:A model for prediction of percent intestinal absorption (%Abs) of neutral molecules was developed based upon surface charges of the molecule calculated by density functional theory (DFT). The surface charges are decomposed into sigma moments which are correlated to a partition coefficient representing transfer of the ...

journal_title：Journal of chemical information and modeling

authors： Jones R,Connolly PC,Klamt A,Diedenhofen M

更新日期：2005-09-01 00:00:00

abstract：:Standardization is used to ensure that the variables in a similarity calculation make an equal contribution to the computed similarity value. This paper compares the use of seven different methods that have been suggested previously for the standardization of integer-valued or real-valued data, comparing the results w...

journal_title：Journal of chemical information and modeling

authors： Chu CW,Holliday JD,Willett P

更新日期：2009-02-01 00:00:00

abstract：:The evaluation of regression QSAR model performance, in fitting, robustness, and external prediction, is of pivotal importance. Over the past decade, different external validation parameters have been proposed: Q(F1)(2), Q(F2)(2), Q(F3)(2), r(m)(2), and the Golbraikh-Tropsha method. Recently, the concordance correlati...

journal_title：Journal of chemical information and modeling

authors： Chirico N,Gramatica P

更新日期：2012-08-27 00:00:00

abstract：:Membrane fusion, a key step in the early stages of virus propagation, allows the release of the viral genome in the host cell cytoplasm. The process is initiated by fusion peptides that are small, hydrophobic components of viral membrane-embedded glycoproteins and are typically conserved within virus families. Here, w...

journal_title：Journal of chemical information and modeling

authors： Borkotoky S,Dey D,Banerjee M

更新日期：2021-01-25 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：: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：:Generation and prioritization of new molecules are the most central part of the drug design process. Matched molecular series analysis (MMSA) has recently been proposed as a formal approach that captures both of these key elements of design. In order to better understand the power of MMSA and its specific limitations,...

journal_title：Journal of chemical information and modeling

authors： Awale M,Riniker S,Kramer C

更新日期：2020-06-22 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：: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

abstract：:Discovery of new antibacterial agents is a never-ending task of medicinal chemistry. Every new drug brings significant improvement to patients with bacterial infections, but prolonged usage of antibacterials leads to the emergence of resistant strains. Therefore, novel active structures with new modes of action are re...

journal_title：Journal of chemical information and modeling

authors： Pogodin PV,Lagunin AA,Rudik AV,Druzhilovskiy DS,Filimonov DA,Poroikov VV

更新日期：2019-11-25 00:00:00

abstract：:In this study, we have developed a two model system to mimic the active and inactive states of a G-protein coupled receptor specifically the alpha1A adrenergic receptor. We have docked two agonists, epinephrine (phenylamine type) and oxymetazoline (imidazoline type), as well as two antagonists, prazosin and 5-methylur...

journal_title：Journal of chemical information and modeling

authors： Asher WB,Hoskins SN,Slasor LA,Morris DH,Cook EM,Bautista DL

更新日期：2007-09-01 00:00:00

abstract：:The human cytochrome P450 (CYP450) isozymes are the most important enzymes in the body to metabolize many endogenous and exogenous substances including environmental toxins and therapeutic drugs. Any unnecessary interactions between a small molecule and CYP450 isozymes may raise a potential to disarm the integrity of ...

journal_title：Journal of chemical information and modeling

authors： Sun H,Veith H,Xia M,Austin CP,Huang R

更新日期：2011-10-24 00:00:00

abstract：:We present our newly developed and highly efficient lossless compression algorithm for trajectories of atom positions and volumetric data. The algorithm is designed as a two-step approach. In the first step, efficient polynomial extrapolation schemes reduce the information entropy of the data by exploiting both spatia...

journal_title：Journal of chemical information and modeling

authors： Brehm M,Thomas M

更新日期：2018-10-22 00:00:00

abstract：:The roles of chemical compounds in biological systems are now systematically analyzed by high-throughput experimental technologies. To automate the processing and interpretation of large-scale data it is necessary to develop bioinformatics methods to extract information from the chemical structures of these small mole...

journal_title：Journal of chemical information and modeling

authors： Oh M,Yamada T,Hattori M,Goto S,Kanehisa M

更新日期：2007-07-01 00:00:00

abstract：:Structure-based virtual screening is highly used in the early stages of drug discovery to identify new putative lead compounds for a given target. However, when a small molecule elicits a biological effect, but its target is unknown, or the side effects it causes arise from its undesired interaction with unknown count...

journal_title：Journal of chemical information and modeling

authors： De Vita S,Lauro G,Ruggiero D,Terracciano S,Riccio R,Bifulco G

更新日期：2019-11-25 00:00:00

abstract：:In this study, two probabilistic machine-learning algorithms were compared for in silico target prediction of bioactive molecules, namely the well-established Laplacian-modified Naïve Bayes classifier (NB) and the more recently introduced (to Cheminformatics) Parzen-Rosenblatt Window. Both classifiers were trained in ...

journal_title：Journal of chemical information and modeling

authors： Koutsoukas A,Lowe R,Kalantarmotamedi Y,Mussa HY,Klaffke W,Mitchell JB,Glen RC,Bender A

更新日期：2013-08-26 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：: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：:Engineering shape-controlled bionanomaterials requires comprehensive understanding of interactions between biomolecules and inorganic surfaces. We explore the origin of facet-selective binding of peptides adsorbed onto Pt(100) and Pt(111) crystallographic planes. Using molecular dynamics simulations, we show that upon...

journal_title：Journal of chemical information and modeling

authors： Ramakrishnan SK,Martin M,Cloitre T,Firlej L,Cuisinier FJ,Gergely C

更新日期：2013-12-23 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：:Identifying drug-target interactions (DTIs) plays an important role in the field of drug discovery, drug side-effects, and drug repositioning. However, in vivo or biochemical experimental methods for identifying new DTIs are extremely expensive and time-consuming. Recently, in silico or various computational methods h...

journal_title：Journal of chemical information and modeling

authors： Xia LY,Yang ZY,Zhang H,Liang Y

更新日期：2019-07-22 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：:Virtual screening is a powerful methodology to search for new small molecule inhibitors against a desired molecular target. Usually, it involves evaluating thousands of compounds (derived from large databases) in order to select a set of potential binders that will be tested in the wet-lab. The number of tested compou...

journal_title：Journal of chemical information and modeling

authors： Radusky L,Ruiz-Carmona S,Modenutti C,Barril X,Turjanski AG,Martí MA

更新日期：2017-08-28 00:00:00

abstract：:Several drugs elicit their therapeutic efficacy by modulating multiple cellular targets and possess varied polypharmacological actions. The identification of the molecular targets of a potent bioactive molecule is essential in determining its overall polypharmacological profile. Experimental procedures are expensive a...

journal_title：Journal of chemical information and modeling

authors： Dutta D,Das R,Mandal C,Mandal C

更新日期：2018-01-22 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：:The prediction of protein-ligand binding affinity has recently been improved remarkably by machine-learning-based scoring functions. For example, using a set of simple descriptors representing the atomic distance counts, the RF-Score improves the Pearson correlation coefficient to about 0.8 on the core set of the PDBb...

journal_title：Journal of chemical information and modeling

authors： Li Y,Yang J

更新日期：2017-04-24 00:00:00