CHARMMing: a new, flexible web portal for CHARMM.

abstract：:Mass spectrometric data are copious and generate a processing burden that is best dealt with programmatically. PythoMS is a collection of tools based on the Python programming language that assist researchers in creating figures and video output that is informative, clear, and visually compelling. The PythoMS framewor...

journal_title：Journal of chemical information and modeling

authors： Yunker LPE,Donnecke S,Ting M,Yeung D,McIndoe JS

更新日期：2019-04-22 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 cannabinoid receptor subtype 2 (CB2) is a promising therapeutic target for blood cancer, pain relief, osteoporosis, and immune system disease. The recent withdrawal of Rimonabant, which targets another closely related cannabinoid receptor (CB1), accentuates the importance of selectivity for the development of CB2 ...

journal_title：Journal of chemical information and modeling

authors： Ma C,Wang L,Yang P,Myint KZ,Xie XQ

更新日期：2013-01-28 00:00:00

abstract：:Congeners are molecules based on the same carbon skeleton but are different by the number of substituents and/or a substitution pattern. Examples are 1-chloronaphthalene, 1,4-dichloronaphthalene, and 1,3,8-trichloronaphthalene. Various persistent organic pollutants (POPs) exist in the environment as families of congen...

journal_title：Journal of chemical information and modeling

authors： Haranczyk M,Urbaszek P,Ng EG,Puzyn T

更新日期：2012-11-26 00:00:00

abstract：:A database has been derived from recently reported [60]fullerene derivatives, and their binding scores with HIV-1 PR have been computed using docking techniques. Computational methods have been used to predict which derivatives may have high binding affinities, and for these compounds biological tests have been perfor...

journal_title：Journal of chemical information and modeling

authors： Durdagi S,Supuran CT,Strom TA,Doostdar N,Kumar MK,Barron AR,Mavromoustakos T,Papadopoulos MG

更新日期：2009-05-01 00:00:00

abstract：:The programs Phase and Catalyst HypoGen are compared for their performance in determining three-dimensional quantitative structure-activity relationships. Eight sets of compounds with measured activity were collected from the public literature and partitioned into suitable training and test sets by an automated proced...

journal_title：Journal of chemical information and modeling

authors： Evans DA,Doman TN,Thorner DA,Bodkin MJ

更新日期：2007-05-01 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：: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：:An ultrafast docking and virtual screening program, CRDOCK, is presented that contains (1) a search engine that can use a variety of sampling methods and an initial energy evaluation function, (2) several energy minimization algorithms for fine tuning the binding poses, and (3) different scoring functions. This modula...

journal_title：Journal of chemical information and modeling

authors： Cortés Cabrera Á,Klett J,Dos Santos HG,Perona A,Gil-Redondo R,Francis SM,Priego EM,Gago F,Morreale A

更新日期：2012-08-27 00:00:00

abstract：:Blockade of human ether-à-go-go related gene (hERG) channel prolongs the duration of the cardiac action potential and is a common reason for drug failure in preclinical safety trials. Therefore, it is of great importance to develop robust in silico tools to predict potential hERG blockers in the early stages of drug d...

journal_title：Journal of chemical information and modeling

authors： Du-Cuny L,Chen L,Zhang S

更新日期：2011-11-28 00:00:00

abstract：:The effects of paclitaxel (PTX) loading fraction and spatial PTX arrangement on poly(γ-glutamyl-glutamate) paclitaxel (PGG-PTX) aggregation were explored using coarse-grained molecular dynamics. Results show that the PTX loading fraction does not significantly impact aggregation, and the spatial PTX arrangement only a...

journal_title：Journal of chemical information and modeling

authors： Peng LX,Yu L,Howell SB,Gough DA

更新日期：2011-12-27 00:00:00

abstract：:Flavins are versatile biological cofactors which catalyze proton-coupled electron transfers (PCET) with varying number and coupling of electrons. Flavin-mediated oxidations of nicotinamide adenine dinucleotide (NADH) and of succinate, initial redox reactions in cellular respiration, were examined here with multiconfig...

journal_title：Journal of chemical information and modeling

authors： Curtolo F,Arantes GM

更新日期：2020-12-28 00:00:00

abstract：:In this work, we present a systematical investigation of the influence of ligand protonation states, stereoisomers, and tautomers on results obtained with the two protein-ligand docking programs GOLD and PLANTS. These different states were generated with a fully automated tool, called SPORES (Structure PrOtonation and...

journal_title：Journal of chemical information and modeling

authors： ten Brink T,Exner TE

更新日期：2009-06-01 00:00:00

abstract：:The molecular structure of four dimeric units (D-E, E-F, F-G, and G-H) of the DEFGH structural unit of heparin, their anionic forms, and their sodium salts have been studied using the B3LYP/6-31+G(d) method. The optimized geometries indicate that the most stable structure of these dimeric units in neutral state is sta...

journal_title：Journal of chemical information and modeling

authors： Remko M,von der Lieth CW

更新日期：2006-07-01 00:00:00

abstract：:Classical nonpolarizable models, normally based on a combination of Lennard-Jones sites and point charges, are extensively used to model thermodynamic properties of fluids, including solvation. An important shortcoming of these models is that they do not explicitly account for polarization effects, i.e., a description...

journal_title：Journal of chemical information and modeling

authors： Barrera MC,Jorge M

更新日期：2020-03-23 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：:HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X...

journal_title：Journal of chemical information and modeling

authors： Riccardi D,Parks JM,Johs A,Smith JC

更新日期：2015-04-27 00:00:00

abstract：:Covalent inhibitors have been gaining increased attention in drug discovery due to their beneficial properties such as long residence time, high biochemical efficiency, and specificity. Optimization of covalent inhibitors is a complex task that involves parallel monitoring of the noncovalent recognition elements and t...

journal_title：Journal of chemical information and modeling

authors： Mihalovits LM,Ferenczy GG,Keserű GM

更新日期：2020-12-28 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：: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：: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：: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：: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 binding affinity and relative maximal efficacy of human A3 adenosine receptor (AR) agonists were each subjected to ligand-based three-dimensional quantitative structure-activity relationship analysis. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) used a...

journal_title：Journal of chemical information and modeling

authors： Kimand SK,Jacobson KA

更新日期：2007-05-01 00:00:00

abstract：:The ligand binding determinants for the angiotensin II type 1 receptor (AT1R), a G protein-coupled receptor (GPCR), have been characterized by means of computer simulations. As a first step, a pharmacophore model of various known AT1R ligands exhibiting a wide range of binding affinities was generated. Second, a struc...

journal_title：Journal of chemical information and modeling

authors： Matsoukas MT,Cordomí A,Ríos S,Pardo L,Tselios T

更新日期：2013-11-25 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：: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

abstract：:Great attention has been paid to the clinical significance of phosphodiesterase 5 (PDE5) inhibitors, such as sildenafil, tadalafil, and vardenafil widely used for erectile dysfunction. However, sildenafil causes side effects on visual functions since it shows similar potencies to inhibit PDE5 and PDE6, whereas tadalaf...

journal_title：Journal of chemical information and modeling

authors： Huang YY,Li Z,Cai YH,Feng LJ,Wu Y,Li X,Luo HB

更新日期：2013-11-25 00:00:00

abstract：:Arachidonic acid is an essential fatty acid in cells, acting as a key inflammatory intermediate in inflammatory reactions. In cardiac tissues, CYP2J2 can adopt arachidonic acid as a major substrate to produce epoxyeicosatrienoic acids (EETs), which can protect endothelial cells from ischemic or hypoxic injuries and ha...

journal_title：Journal of chemical information and modeling

authors： Cong S,Ma XT,Li YX,Wang JF

更新日期：2013-06-24 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