Training a scoring function for the alignment of small molecules.

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：:Development of accurate force field parameters for molecular ions in the context of a polarizable energy function based on the classical Drude oscillator is a crucial step toward an accurate polarizable model for modeling and simulations of biological macromolecules. Toward this goal we have undertaken a hierarchical ...

journal_title：Journal of chemical information and modeling

authors： Lin FY,Lopes PEM,Harder E,Roux B,MacKerell AD Jr

更新日期：2018-05-29 00:00:00

abstract：:Virtual screening of small molecules against a protein target often identifies the correct pose, but the ranking in terms of binding energy remains a difficult problem, resulting in unacceptable numbers of false positives and negatives. To investigate this problem, the performance of three docking programs, FRED, QXP/...

journal_title：Journal of chemical information and modeling

authors： Deng W,Verlinde CL

更新日期：2008-10-01 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：: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：: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：:We examine the sensitivity of folding molecular dynamics simulations on the choice between three variants of the same force field (the AMBER99SB force field and its ILDN, NMR-ILDN, and STAR-ILDN variants). Using two different peptide systems (a marginally stable helical peptide and a β-hairpin) and a grand total of mo...

journal_title：Journal of chemical information and modeling

authors： Serafeim AP,Salamanos G,Patapati KK,Glykos NM

更新日期：2016-10-24 00:00:00

abstract：:A major concern of chemogenomics is to associate drug activity with biological variables. Several reports have clustered cell line drug activity profiles as well as drug activity-gene expression correlation profiles and noted that the resulting groupings differ but still reflect mechanism of action. The present paper ...

journal_title：Journal of chemical information and modeling

authors： Andersson CR,Fryknäs M,Rickardson L,Larsson R,Isaksson A,Gustafsson MG

更新日期：2007-01-01 00:00:00

abstract：:Previously, stereoselective hydroxylation of α-ionone by Cytochrome P450 BM3 mutants M01 A82W and M11 L437N was observed. While both mutants hydroxylate α-ionone in a regioselective manner at the C3 position, M01 A82W catalyzes formation of trans-3-OH-α-ionone products whereas M11 L437N exhibits opposite stereoselecti...

journal_title：Journal of chemical information and modeling

authors： de Beer SB,Venkataraman H,Geerke DP,Oostenbrink C,Vermeulen NP

更新日期：2012-08-27 00:00:00

abstract：:Human type II topoisomerases, molecular motors that alter the DNA topology, are a major target of modern chemotherapy. Groups of catalytic inhibitors represent a new approach to overcome the known limitations of topoisomerase II poisons such as cardiotoxicity and induction of secondary tumors. Here, we present a class...

journal_title：Journal of chemical information and modeling

authors： Bergant Loboda K,Janežič M,Štampar M,Žegura B,Filipič M,Perdih A

更新日期：2020-07-27 00:00:00

abstract：:Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishin...

journal_title：Journal of chemical information and modeling

authors： Zhang Q,Xu Z,Shi J,Zhu W

更新日期：2017-07-24 00:00:00

abstract：:The viral NS5B RNA-dependent RNA-polymerase (RdRp) is one of the best-studied and promising targets for the development of novel therapeutics against hepatitis C virus (HCV). Allosteric inhibition of this enzyme has emerged as a viable strategy toward blocking replication of viral RNA in cell based systems. Herein, we...

journal_title：Journal of chemical information and modeling

authors： Musmuca I,Caroli A,Mai A,Kaushik-Basu N,Arora P,Ragno R

更新日期：2010-04-26 00:00:00

abstract：:Target-oriented substructure-based virtual screening (sSBVS) of molecules is a promising approach in drug discovery. Yet, there are doubts whether sSBVS is suitable also for extrapolation, that is, for detecting molecules that are very different from those used for training. Herein, we evaluate the predictive power of...

journal_title：Journal of chemical information and modeling

authors： Biniashvili T,Schreiber E,Kliger Y

更新日期：2012-03-26 00:00:00

abstract：:The recent article "Evaluation of pK(a) Estimation Methods on 211 Druglike Compounds" ( Manchester, J.; et al. J. Chem Inf. Model. 2010, 50, 565-571 ) reports poor results for the program Epik. Here, we highlight likely sources for the poor performance and describe work done to improve the performance. Running Epik in...

journal_title：Journal of chemical information and modeling

authors： Shelley JC,Calkins D,Sullivan AP

更新日期：2011-01-24 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：: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：:Random Forest regression (RF), Partial-Least-Squares (PLS) regression, Support Vector Machines (SVM), and Artificial Neural Networks (ANN) were used to develop QSPR models for the prediction of aqueous solubility, based on experimental data for 988 organic molecules. The Random Forest regression model predicted aqueou...

journal_title：Journal of chemical information and modeling

authors： Palmer DS,O'Boyle NM,Glen RC,Mitchell JB

更新日期：2007-01-01 00:00:00

abstract：:Up to now, publicly available data sets to build and evaluate Ames mutagenicity prediction tools have been very limited in terms of size and chemical space covered. In this report we describe a new unique public Ames mutagenicity data set comprising about 6500 nonconfidential compounds (available as SMILES strings and...

journal_title：Journal of chemical information and modeling

authors： Hansen K,Mika S,Schroeter T,Sutter A,ter Laak A,Steger-Hartmann T,Heinrich N,Müller KR

更新日期：2009-09-01 00:00:00

abstract：:The antiproliferative factor (APF) involved in interstitial cystitis is a glycosylated nonapeptide (TVPAAVVVA) containing a sialylated core 1 α-O-disaccharide linked to the N-terminal threonine. The chemical structure of APF was deduced using spectroscopic techniques and confirmed using total synthesis. The synthetic ...

journal_title：Journal of chemical information and modeling

authors： Mallajosyula SS,Adams KM,Barchi JJ,MacKerell AD

更新日期：2013-05-24 00:00:00

abstract：:A new variable selection wrapper method named the Monte Carlo variable selection (MCVS) method was developed utilizing the framework of the Monte Carlo cross-validation (MCCV) approach. The MCVS method reports the variable selection results in the most conventional and common measure of statistical hypothesis testing,...

journal_title：Journal of chemical information and modeling

authors： Konovalov DA,Sim N,Deconinck E,Vander Heyden Y,Coomans D

更新日期：2008-02-01 00:00:00

abstract：:The primary goal of this project was to evaluate the performance of the Standard and Enforced Geometry Optimization (SEGO) method which we have recently developed. The SEGO method has been designed for an automatic location of multiple minima on the molecular Potential Energy Surface (PES), and its usefulness has been...

journal_title：Journal of chemical information and modeling

authors： Brzyska A,Woliński K

更新日期：2019-08-26 00:00:00

abstract：:The purpose of this investigation is to contribute to the development of new anticonvulsant drugs to treat patients with refractory epilepsy. We applied a virtual screening protocol that involved the search into molecular databases of new compounds and known drugs to find small molecules that interact with the open co...

journal_title：Journal of chemical information and modeling

authors： Palestro PH,Enrique N,Goicoechea S,Villalba ML,Sabatier LL,Martin P,Milesi V,Bruno Blanch LE,Gavernet L

更新日期：2018-07-23 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：:A new radial space-filling method for visualizing cluster hierarchies is presented. The method, referred to as a radial clustergram, arranges the clusters into a series of layers, each representing a different level of the tree. It uses adjacency of nodes instead of links to represent parent-child relationships and al...

journal_title：Journal of chemical information and modeling

authors： Agrafiotis DK,Bandyopadhyay D,Farnum M

更新日期：2007-01-01 00:00:00

abstract：:This paper is an overview of the most significant and impactful interpretation approaches of quantitative structure-activity relationship (QSAR) models, their development, and application. The evolution of the interpretation paradigm from "model → descriptors → (structure)" to "model → structure" is indicated. The lat...

journal_title：Journal of chemical information and modeling

authors： Polishchuk P

更新日期：2017-11-27 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：:Engineered nanomaterials (ENMs) are increasingly infiltrating our lives as a result of their applications across multiple fields. However, ENM formulations may result in the modulation of pathways and mechanisms of toxic action that endanger human health and the environment. Alternative testing methods such as in sili...

journal_title：Journal of chemical information and modeling

authors： Chomenidis C,Drakakis G,Tsiliki G,Anagnostopoulou E,Valsamis A,Doganis P,Sopasakis P,Sarimveis H

更新日期：2017-09-25 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：:In this study, we compared the contributions of polar and nonpolar interactions to the solvation free energy of a solute in solvent, which is decomposed into four different terms based on the nature of interactions: (i) electrostatic solvation free energy term counting for the work done to move solute charges from fix...

journal_title：Journal of chemical information and modeling

authors： Izairi R,Kamberaj H

更新日期：2017-10-23 00:00:00

abstract：:Protein-protein interactions are central to many biological processes, from intracellular communication to cytoskeleton assembly, and therefore represent an important class of targets for new therapeutics. The most common secondary structure in natural proteins is an α-helix. Small molecules seem to be attractive cand...

journal_title：Journal of chemical information and modeling

authors： Santos JS,Voisin-Chiret AS,Burzicki G,Sebaoun L,Sebban M,Lohier JF,Legay R,Oulyadi H,Bureau R,Rault S

更新日期：2012-02-27 00:00:00