Comparison of several molecular docking programs: pose prediction and virtual screening accuracy.

abstract：:Cytochrome P450 2D6 (CYP2D6) is used to develop an approach for predicting affinity and relevant binding conformation(s) for highly flexible binding sites. The approach combines the use of docking scores and compound properties as attributes in building a neural network (NN) model. It begins by identifying segments of...

journal_title：Journal of chemical information and modeling

authors： Bazeley PS,Prithivi S,Struble CA,Povinelli RJ,Sem DS

更新日期：2006-11-01 00:00:00

abstract：:This study has assessed the use of consensus regression, as compared to single multiple linear regression, models for the development of quantitative structure-activity relationships (QSARs). To provide a comparison, four data sets of varying size and complexity were analyzed: silastic membrane flux, toxicity of pheno...

journal_title：Journal of chemical information and modeling

authors： Hewitt M,Cronin MT,Madden JC,Rowe PH,Johnson C,Obi A,Enoch SJ

更新日期：2007-07-01 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：:One of the largest commercial applications of enzymes and surfactants is as main components in modern detergents. The high concentration of surfactant compounds usually present in detergents can, however, negatively affect the enzymatic activity. To remedy this drawback, it is of great importance to characterize the i...

journal_title：Journal of chemical information and modeling

authors： Kjølbye LR,Laustsen A,Vestergaard M,Periole X,De Maria L,Svendsen A,Coletta A,Schiøtt B

更新日期：2019-05-28 00:00:00

abstract：:Herein we investigate whether QM/MM could prove useful as a tool to study the often subtle binding phenomena found within pharmaceutical drug discovery programs. The goal of this investigation is to determine whether it is possible to employ high level QM/MM calculations to answer specific questions around a binding e...

journal_title：Journal of chemical information and modeling

authors： Gleeson MP,Gleeson D

更新日期：2009-03-01 00:00:00

abstract：:Nitric oxide (NO) is an important signaling molecule produced by a family of enzymes called nitric oxide synthases (NOS). Because NO is involved in various pathological conditions, the development of potent and isoform-selective NOS inhibitors is an important challenge. In the present study, the dimer of oxygenase dom...

journal_title：Journal of chemical information and modeling

authors： Floquet N,Hernandez JF,Boucher JL,Martinez J

更新日期：2011-06-27 00:00:00

abstract：:Cathepsin A is a mammalian lysosomal enzyme that catalyzes the hydrolysis of the carboxy-terminal amino acids of polypeptides and also regulates beta-galactosidase and neuraminidase-1 activities through the formation of a multienzymic complex in lysosomes. Human cathepsin A (hCathA), yeast carboxypeptidase (CPY), and ...

journal_title：Journal of chemical information and modeling

authors： Yoshida T,Lepp Z,Kadota Y,Satoh Y,Itoh K,Chuman H

更新日期：2006-09-01 00:00:00

abstract：:As a result of the widespread industrial use of polychlorinated hydrocarbons, they have accumulated in nearly all types of environmental compartments, especially in aquatic systems. Particularly, chloroaromatics are among the most undesirable industrial effluents because of their persistence and toxicity. To predict c...

journal_title：Journal of chemical information and modeling

authors： Ivanciuc T,Ivanciuc O,Klein DJ

更新日期：2005-07-01 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：: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：:A kinetic, reactivity-binding model has been proposed to predict the regioselectivity of substrates meditated by the CYP1A2 enzyme, which is responsible for the metabolism of planar-conjugated compounds such as caffeine. This model consists of a docking simulation for binding energy and a semiempirical molecular orbit...

journal_title：Journal of chemical information and modeling

authors： Jung J,Kim ND,Kim SY,Choi I,Cho KH,Oh WS,Kim DN,No KT

更新日期：2008-05-01 00:00:00

abstract：:An important issue in developing protein-ligand docking methods is how to incorporate receptor flexibility. Consideration of receptor flexibility using an ensemble of precompiled receptor conformations or by employing an effectively enlarged binding pocket has been reported to be useful. However, direct consideration ...

journal_title：Journal of chemical information and modeling

authors： Shin WH,Seok C

更新日期：2012-12-21 00:00:00

abstract：:We investigate unexpectedly short non-covalent distances (<85% of the sum of van der Waals radii) in X-ray crystal structures of proteins. We curate over 11 000 high-quality protein crystal structures and an ultra-high-resolution (1.2 Å or better) subset containing >900 structures. Although our non-covalent distance c...

journal_title：Journal of chemical information and modeling

authors： Qi HW,Kulik HJ

更新日期：2019-05-28 00:00:00

abstract：:A compound's synthetic accessibility (SA) is an important aspect of drug design, since in some cases computer-designed compounds cannot be synthesized. There have been several reports on SA prediction, most of which have focused on the difficulties of synthetic reactions based on retro-synthesis analyses, reaction dat...

journal_title：Journal of chemical information and modeling

authors： Fukunishi Y,Kurosawa T,Mikami Y,Nakamura H

更新日期：2014-12-22 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：:Sixteen FDA-approved drugs were investigated to elucidate their mechanisms of action (MOAs) and clinical functions by pathway analysis based on retrieved drug targets interacting with or affected by the investigated drugs. Protein and gene targets and associated pathways were obtained by data-mining of public database...

journal_title：Journal of chemical information and modeling

authors： Pan Y,Cheng T,Wang Y,Bryant SH

更新日期：2014-02-24 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 determination of the validity of a QSAR model when applied to new compounds is an important concern in the field of QSAR and QSPR modeling. Various scoring techniques can be applied to specific types of models. We present a technique with which we can state whether a new compound will be well predicted by a previo...

journal_title：Journal of chemical information and modeling

authors： Guha R,Jurs PC

更新日期：2005-01-01 00:00:00

abstract：:In structure-based drug design, scoring functions are often employed to evaluate protein-ligand interactions. A variety of scoring functions have been developed so far, and thus, some objective benchmarks are desired for assessing their strength and weakness. The comparative assessment of scoring functions (CASF) benc...

journal_title：Journal of chemical information and modeling

authors： Su M,Yang Q,Du Y,Feng G,Liu Z,Li Y,Wang R

更新日期：2019-02-25 00:00:00

abstract：:The interaction between small molecules and proteins is one of the major concerns for structure-based drug design because the principles of protein-ligand interactions and molecular recognition are not thoroughly understood. Fortunately, the analysis of protein-ligand complexes in the Protein Data Bank (PDB) enables u...

journal_title：Journal of chemical information and modeling

authors： Wang L,Xie Z,Wipf P,Xie XQ

更新日期：2011-04-25 00:00:00

abstract：:With continually increased computer power, molecular mechanics force field-based approaches, such as the endpoint methods of molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and molecular mechanics generalized Born surface area (MM-GBSA), have been routinely applied in both drug lead identification and opt...

journal_title：Journal of chemical information and modeling

authors： Hao D,He X,Ji B,Zhang S,Wang J

更新日期：2020-12-28 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：:This paper introduces the concept of an isomer network based on the reaction step counts between pairs of isomers as an alternative means to view and analyze isomer space. The computation of isomer networks is computationally expensive with respect to both run time and memory. Accordingly, this paper focuses on the de...

journal_title：Journal of chemical information and modeling

authors： Kouri TM,Awale M,Slyby JK,Reymond JL,Mehta DP

更新日期：2014-01-27 00:00:00

abstract：:Advances in computer-aided translation technology have made tremendous progress in accuracy in the past few years. Chemical Abstracts Service of the American Chemical Society summarizes scientific works from more than 50 languages and allows the users to search papers in nine selected languages. Currently, only the ab...

journal_title：Journal of chemical information and modeling

authors： Wahab MF,Zulfiqar S,Sarwar MI,Lieberwirth I

更新日期：2020-07-27 00:00:00

abstract：:Machine learning has exhibited powerful capabilities in many areas. However, machine learning models are mostly database dependent, requiring a new model if the database changes. Therefore, a universal model is highly desired to accommodate the widest variety of databases. Fortunately, this universality may be achieve...

journal_title：Journal of chemical information and modeling

authors： Li W,Miao W,Cui J,Fang C,Su S,Li H,Hu L,Lu Y,Chen G

更新日期：2019-05-28 00:00:00

abstract：:Factor Xa inhibitors are innovative anticoagulant agents that provide a better safety/efficacy profile compared to other anticoagulative drugs. A chemical feature-based modeling approach was applied to identify crucial pharmacophore patterns from 3D crystal structures of inhibitors bound to human factor Xa (Pdb entrie...

journal_title：Journal of chemical information and modeling

authors： Krovat EM,Frühwirth KH,Langer T

更新日期：2005-01-01 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：:Chemical structure extraction from documents remains a hard problem because of both false positive identification of structures during segmentation and errors in the predicted structures. Current approaches rely on handcrafted rules and subroutines that perform reasonably well generally but still routinely encounter s...

journal_title：Journal of chemical information and modeling

authors： Staker J,Marshall K,Abel R,McQuaw CM

更新日期：2019-03-25 00:00:00

abstract：:Thermoplastic polyurethanes (TPUs) are designed using a large variety of basic building blocks but are only synthesized in a limited number of solvent systems. Understanding the behavior of the copolymers in a selected solvent system is of particular interest to tune the intricate balance of microphase separation/mixi...

journal_title：Journal of chemical information and modeling

authors： Avaz Seven S,Oguz O,Menceloglu YZ,Atilgan C

更新日期：2019-05-28 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