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：: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：:In this DFT study, activities of 11 different N2O4, N2O3, and NO2 core containing Zr(IV) complexes, 4,13-diaza-18-crown-6 (I'N2O4), 1,4,10-trioxa-7,13-diazacyclopentadecane (I'N2O3), and 2-(2-methoxy)ethanol (I'NO2), respectively, and their analogues in peptide hydrolysis have been investigated. Based on the experimen...

journal_title：Journal of chemical information and modeling

authors： Zhang T,Sharma G,Paul TJ,Hoffmann Z,Prabhakar R

更新日期：2017-05-22 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

abstract：:Optimization of ligand binding affinity to the target protein of interest is a primary objective in small-molecule drug discovery. Until now, the prediction of binding affinities by computational methods has not been widely applied in the drug discovery process, mainly because of its lack of accuracy and reproducibili...

journal_title：Journal of chemical information and modeling

authors： Wan S,Bhati AP,Skerratt S,Omoto K,Shanmugasundaram V,Bagal SK,Coveney PV

更新日期：2017-04-24 00:00:00

abstract：:Large ring cyclodextrins have become increasingly important for drug delivery applications. In this work, we have performed replica-exchange molecular dynamics simulations using both implicit and explicit water solvation models to study the conformational diversity of iota-cyclodextrin containing 14 α-1,4 glycosidic l...

journal_title：Journal of chemical information and modeling

authors： Khuntawee W,Kunaseth M,Rungnim C,Intagorn S,Wolschann P,Kungwan N,Rungrotmongkol T,Hannongbua S

更新日期：2017-04-24 00:00:00

abstract：:The balance between structural stability and functional plasticity in proteins that share common three-dimensional folds is the key factor that drives protein evolvability. The ability to distinguish the parts of homologous proteins that underlie common structural organization patterns from the parts acting as regulat...

journal_title：Journal of chemical information and modeling

authors： Rinaldi S,Gori A,Annovazzi C,Ferrandi EE,Monti D,Colombo G

更新日期：2017-04-24 00:00:00

abstract：:Development of coarse-grained (CG) molecular dynamics models is often a laborious process which commonly relies upon approximations to similar models, rather than systematic parametrization. PyCGTOOL automates much of the construction of CG models via calculation of both equilibrium values and force constants of inter...

journal_title：Journal of chemical information and modeling

authors： Graham JA,Essex JW,Khalid S

更新日期：2017-04-24 00:00:00

abstract：:SIRT2, which is a NAD+ (nicotinamide adenine dinucleotide) dependent deacetylase, has been demonstrated to play an important role in the occurrence and development of a variety of diseases such as cancer, ischemia-reperfusion, and neurodegenerative diseases. Small molecule inhibitors of SIRT2 are thought to be potenti...

journal_title：Journal of chemical information and modeling

authors： Huang S,Song C,Wang X,Zhang G,Wang Y,Jiang X,Sun Q,Huang L,Xiang R,Hu Y,Li L,Yang S

更新日期：2017-04-24 00:00:00

abstract：:Membrane transporters play a crucial role in determining fate of administered drugs in a biological system. Early identification of plausible transporters for a drug molecule can provide insights into its therapeutic, pharmacokinetic, and toxicological profiles. In the present study, predictive models for classifying ...

journal_title：Journal of chemical information and modeling

authors： Shaikh N,Sharma M,Garg P

更新日期：2017-03-27 00:00:00

abstract：:In this study, we used the Martini Coarse-Grained model with no applied restraints to predict the binding mode of some peptides to G-Protein Coupled Receptors (GPCRs). Both the Neurotensin-1 and the chemokine CXCR4 receptors were used as test cases. Their ligands, NTS8-13 and CVX15 peptides, respectively, were initial...

journal_title：Journal of chemical information and modeling

authors： Delort B,Renault P,Charlier L,Raussin F,Martinez J,Floquet N

更新日期：2017-03-27 00:00:00

abstract：:Screening large libraries of chemicals has been an efficient strategy to discover bioactive compounds; however a portion of the potential for success is limited to the available libraries. Synergizing combinatorial and computational chemistries has emerged as a time-efficient strategy to explore the chemical space mor...

journal_title：Journal of chemical information and modeling

authors： Pottel J,Moitessier N

更新日期：2017-03-27 00:00:00

abstract：:Calcium is involved in important intracellular processes, such as intracellular signaling from cell membrane receptors to the nucleus. Typically, calcium levels are kept at less than 100 nM in the nucleus and cytosol, but some calcium is stored in the endoplasmic reticulum (ER) lumen for rapid release to activate intr...

journal_title：Journal of chemical information and modeling

authors： Mukherjee S,Karolak A,Debant M,Buscaglia P,Renaudineau Y,Mignen O,Guida WC,Brooks WH

更新日期：2017-02-27 00:00:00

abstract：:Computer programs for structure diagram generation (SDG) are indispensable cheminformatic tools that translate one- or three-dimensional (1D or 3D) chemical structure data stored in electronic formats to human-readable 2D depictions. Although many such programs are known, only a moderate part of chemical space can be ...

journal_title：Journal of chemical information and modeling

authors： Frączek T

更新日期：2016-12-27 00:00:00

abstract：:The human androgen receptor (AR) is a ligand-activated transcription factor that plays a pivotal role in the development and progression of prostate cancer (PCa). Many forms of castration-resistant prostate cancer (CRPC) still rely on the AR for survival. Currently used antiandrogens face clinical limitations as drug ...

journal_title：Journal of chemical information and modeling

authors： Paul N,Carabet LA,Lallous N,Yamazaki T,Gleave ME,Rennie PS,Cherkasov A

更新日期：2016-12-27 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 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：:The goal of the present study was to ascertain the differential performance of a long molecular dynamics trajectory versus several shorter ones starting from different points in the phase space and covering the same sampling time. For this purpose, we selected the 16-mer peptide Bak16BH3 as a model for study and carri...

journal_title：Journal of chemical information and modeling

authors： Perez JJ,Tomas MS,Rubio-Martinez J

更新日期：2016-10-24 00:00:00

abstract：:The d-Ala:d-Lac ligase, VanA, plays a critical role in the resistance of vancomycin. Indeed, it is involved in the synthesis of a peptidoglycan precursor, to which vancomycin cannot bind. The reaction catalyzed by VanA requires the opening of the so-called "ω-loop", so that the substrates can enter the active site. He...

journal_title：Journal of chemical information and modeling

authors： Duclert-Savatier N,Bouvier G,Nilges M,Malliavin TE

更新日期：2016-09-26 00:00:00

abstract：:HIV-1 replication requires binding to occur between Trans-activation Response Element (TAR) RNA and the TAT protein. This TAR-TAT binding depends on the conformation of TAR, and therapeutic development has attempted to exploit this dynamic behavior. Here we simulate TAR dynamics in the context of mutations inhibiting ...

journal_title：Journal of chemical information and modeling

authors： Krawczyk K,Sim AY,Knapp B,Deane CM,Minary P

更新日期：2016-09-26 00:00:00

abstract：:A MMGBSA variant (here referred to as Nwat-MMGBSA), based on the inclusion of a certain number of explicit water molecules (Nwat) during the calculations, has been tested on a set of 20 protein-protein complexes, using the correlation between predicted and experimental binding energy as the evaluation metric. Besides ...

journal_title：Journal of chemical information and modeling

authors： Maffucci I,Contini A

更新日期：2016-09-26 00:00:00

abstract：:The membrane permeability of cyclic peptides and peptidomimetics, which are generally larger and more complex than typical drug molecules, is likely strongly influenced by the conformational behavior of these compounds in polar and apolar environments. The size and complexity of peptides often limit their bioavailabil...

journal_title：Journal of chemical information and modeling

authors： Witek J,Keller BG,Blatter M,Meissner A,Wagner T,Riniker S

更新日期：2016-08-22 00:00:00

abstract：:There is a growing public concern about the lack of reproducibility of experimental data published in peer-reviewed scientific literature. Herein, we review the most recent alerts regarding experimental data quality and discuss initiatives taken thus far to address this problem, especially in the area of chemical geno...

journal_title：Journal of chemical information and modeling

authors： Fourches D,Muratov E,Tropsha A

更新日期：2016-07-25 00:00:00

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：:We present an induced fit docking approach called Adaptive BP-Dock that integrates perturbation response scanning (PRS) with the flexible docking protocol of RosettaLigand in an adaptive manner. We first perturb the binding pocket residues of a receptor and obtain a new conformation based on the residue response fluct...

journal_title：Journal of chemical information and modeling

authors： Bolia A,Ozkan SB

更新日期：2016-04-25 00:00:00

abstract：:Virtual screening is routinely used to discover new ligands and in particular new ligand chemotypes for G protein-coupled receptors (GPCRs). To prepare for a virtual screen, we often tailor a docking protocol that will enable us to select the best candidates for further screening. To aid this, we created GPCR-Bench, a...

journal_title：Journal of chemical information and modeling

authors： Weiss DR,Bortolato A,Tehan B,Mason JS

更新日期：2016-04-25 00:00:00

abstract：:Although there are several databases that contain data on many metabolites and reactions in biochemical pathways, there is still a big gap in the numbers between experimentally identified enzymes and metabolites. It is supposed that many catalytic enzyme genes are still unknown. Although there are previous studies tha...

journal_title：Journal of chemical information and modeling

authors： Moriya Y,Yamada T,Okuda S,Nakagawa Z,Kotera M,Tokimatsu T,Kanehisa M,Goto S

更新日期：2016-03-28 00:00:00

abstract：:Antimicrobial peptides (AMPs) have emerged as promising therapeutic alternatives to fight against the diverse infections caused by different pathogenic microorganisms. In this context, theoretical approaches in bioinformatics have paved the way toward the creation of several in silico models capable of predicting anti...

journal_title：Journal of chemical information and modeling

authors： Speck-Planche A,Kleandrova VV,Ruso JM,Cordeiro MN

更新日期：2016-03-28 00:00:00

abstract：:Increased reports of oseltamivir (OTV)-resistant strains of the influenza virus, such as the H274Y mutation on its neuraminidase (NA), have created some cause for concern. Many studies have been conducted in the attempt to uncover the mechanism of OTV resistance in H274Y NA. However, most of the reported studies on H2...

journal_title：Journal of chemical information and modeling

authors： Yusuf M,Mohamed N,Mohamad S,Janezic D,Damodaran KV,Wahab HA

更新日期：2016-01-25 00:00:00

abstract：:Interfacial hydration strongly influences interactions between biomolecules. For example, drug-target complexes are often stabilized by hydration networks formed between hydrophilic residues and water molecules at the interface. Exhaustive exploration of hydration networks is challenging for experimental as well as th...

journal_title：Journal of chemical information and modeling

authors： Jeszenői N,Bálint M,Horváth I,van der Spoel D,Hetényi C

更新日期：2016-01-25 00:00:00

abstract：:Human cannabinoid type 1 (CB1) G-protein coupled receptor is a potential therapeutic target for obesity. The previously predicted and experimentally validated ensemble of ligand-free conformations of CB1 [Scott, C. E. et al. Protein Sci. 2013 , 22 , 101 - 113 ; Ahn, K. H. et al. Proteins 2013 , 81 , 1304 - 1317] are u...

journal_title：Journal of chemical information and modeling

authors： Scott CE,Ahn KH,Graf ST,Goddard WA 3rd,Kendall DA,Abrol R

更新日期：2016-01-25 00:00:00

abstract：:The recognition of peptide/MHC by T-cell receptors is one of the most important interactions in the adaptive immune system. A large number of computational studies have investigated the structural dynamics of this interaction. However, to date only limited attention has been paid to differences between the dynamics of...

journal_title：Journal of chemical information and modeling

authors： Knapp B,Deane CM

更新日期：2016-01-25 00:00:00

abstract：:Peptides that bind to ion channels have attracted much interest as potential lead molecules for the development of new drugs and insecticides. However, the structure determination of large peptide-channel complexes using experimental methods is challenging. Thus structural models are often derived from combining exper...

journal_title：Journal of chemical information and modeling

authors： Deplazes E,Davies J,Bonvin AM,King GF,Mark AE

更新日期：2016-01-25 00:00:00

abstract：:The Torsion Library contains hundreds of rules for small molecule conformations which have been derived from the Cambridge Structural Database (CSD) and are curated by molecular design experts. The torsion rules are encoded as SMARTS patterns and categorize rotatable bonds via a traffic light coloring scheme. We have ...

journal_title：Journal of chemical information and modeling

authors： Guba W,Meyder A,Rarey M,Hert J

更新日期：2016-01-25 00:00:00

abstract：:An in silico screening procedure was performed to select new inhibitors of glycogen synthase kinase 3β (GSK-3β), a serine/threonine protein kinase that in the last two decades has emerged as a key target in drug discovery, having been implicated in multiple cellular processes and linked with the pathogenesis of severa...

journal_title：Journal of chemical information and modeling

authors： Ombrato R,Cazzolla N,Mancini F,Mangano G

更新日期：2015-12-28 00:00:00

abstract：:Piperine, the bioactive phytochemical from black pepper (Piper nigrum L.), is a nontoxic natural compound exhibiting many physiological and pharmacological properties. They include antioxidant, anti-inflammatory, antimutagenic, antitumor, antiapoptotic, antigenotoxic, antiarthritic, antifungal, antimicrobial, antidepr...

journal_title：Journal of chemical information and modeling

authors： Haris P,Mary V,Haridas M,Sudarsanakumar C

更新日期：2015-12-28 00:00:00

abstract：:Extending the original training data with simulated unobserved data points has proven powerful to increase both the generalization ability of predictive models and their robustness against changes in the structure of data (e.g., systematic drifts in the response variable) in diverse areas such as the analysis of spect...

journal_title：Journal of chemical information and modeling

authors： Cortes-Ciriano I,Bender A

更新日期：2015-12-28 00:00:00

abstract：:Telomere maintenance is a universal cancer hallmark, and small molecules that disrupt telomere maintenance generally have anticancer properties. Since the vast majority of cancer cells utilize telomerase activity for telomere maintenance, the enzyme has been considered as an anticancer drug target. Recently, rational ...

journal_title：Journal of chemical information and modeling

authors： Shirgahi Talari F,Bagherzadeh K,Golestanian S,Jarstfer M,Amanlou M

更新日期：2015-12-28 00:00:00

abstract：:The protection exerted by 3,5-dihydroxy-4-methoxybenzyl alcohol (DHMBA), a phenolic compound recently isolated from the Pacific oyster, against oxidative stress (OS) is investigated using the density functional theory. Our results indicate that DHMBA is an outstanding peroxyl radical scavenger, being about 15 times an...

journal_title：Journal of chemical information and modeling

authors： Villuendas-Rey Y,Alvarez-Idaboy JR,Galano A

更新日期：2015-12-28 00:00:00

abstract：:Protein arginine methyltransferases (PRMTs) catalyze the posttranslational methylation of arginine, which is important in a range of biological processes, including epigenetic regulation, signal transduction, and cancer progression. Although previous studies of PRMT1 mutants suggest that the dimerization arm and the N...

journal_title：Journal of chemical information and modeling

authors： Zhou R,Xie Y,Hu H,Hu G,Patel VS,Zhang J,Yu K,Huang Y,Jiang H,Liang Z,Zheng YG,Luo C

更新日期：2015-12-28 00:00:00