Periodic cages.

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 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：:Novel statistical potentials derived from known protein structures are presented. They are designed to describe cation-pi and amino-pi interactions between a positively charged amino acid or an amino acid carrying a partially charged amino group and an aromatic moiety. These potentials are based on the propensity of r...

journal_title：Journal of chemical information and modeling

authors： Gilis D,Biot C,Buisine E,Dehouck Y,Rooman M

更新日期：2006-03-01 00:00:00

abstract：:The failure of default scoring functions to ensure virtual screening enrichment is a persistent problem for the molecular docking algorithms used in structure-based drug discovery. To remedy this problem, elaborate rescoring and postprocessing schemes have been developed with a varying degree of success, specificity, ...

journal_title：Journal of chemical information and modeling

authors： Kurkinen ST,Lätti S,Pentikäinen OT,Postila PA

更新日期：2019-08-26 00:00:00

abstract：:Theoretical calculation of equilibrium dissociation constants is a very computationally demanding and time-consuming process since it requires an extremely accurate computation of the solvation free energy changes for each of the species involved. By correlating the minimum surface electrostatic potential (VS,min) on ...

journal_title：Journal of chemical information and modeling

authors： Sandoval-Lira J,Mondragón-Solórzano G,Lugo-Fuentes LI,Barroso-Flores J

更新日期：2020-03-23 00:00:00

abstract：:Pharmacophore search is a key component of many drug discovery efforts. Pharmer is a new computational approach to pharmacophore search that scales with the breadth and complexity of the query, not the size of the compound library being screened. Two novel methods for organizing pharmacophore data, the Pharmer KDB-tre...

journal_title：Journal of chemical information and modeling

authors： Koes DR,Camacho CJ

更新日期：2011-06-27 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：: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：:Molecular docking programs are widely used modeling tools for predicting ligand binding modes and structure based virtual screening. In this study, six molecular docking programs (DOCK, FlexX, GLIDE, ICM, PhDOCK, and Surflex) were evaluated using metrics intended to assess docking pose and virtual screening accuracy. ...

journal_title：Journal of chemical information and modeling

authors： Cross JB,Thompson DC,Rai BK,Baber JC,Fan KY,Hu Y,Humblet C

更新日期：2009-06-01 00:00:00

abstract：:Soluble low-molecular-weight oligomers formed during the early stage of amyloid aggregation are considered the major toxic species in amyloidosis. The structure-function relationship between oligomeric assemblies and the cytotoxicity in amyloid diseases are still elusive due to the heterogeneous and transient nature o...

journal_title：Journal of chemical information and modeling

authors： Sun Y,Huang J,Duan X,Ding F

更新日期：2021-01-14 00:00:00

abstract：:Functional diversity of the three-finger-protein domain (TFPD) had been acquired via hypervariability of some sequence positions and extensive insertion/deletion of short AA-segments that caused multidimensional drift of several sequence attributes such as the overall (HI) and local hydrophobicity levels, the isoelect...

journal_title：Journal of chemical information and modeling

authors： Galat A

更新日期：2015-09-28 00:00:00

abstract：:A new methodology to describe the interactions in "receptor-ligand" complexes is presented. The methodology is based on a combination of the 3D/4D QSAR BiS/MC and CoCon algorithms. The first algorithm performs the restricted docking of compounds to receptor pockets. The second determines the relationships between the ...

journal_title：Journal of chemical information and modeling

authors： Potemkin VA,Pogrebnoy AA,Grishina MA

更新日期：2009-06-01 00:00:00

abstract：:The study of chromatographic retention of natural products can be used to increase their identification speed in complex biological matrices. In this work, six variables were used to study the retention behavior in reversed phase liquid chromatography of 39 sesquiterpene lactones (SL) from an in-house database using c...

journal_title：Journal of chemical information and modeling

authors： Oliveira TB,Gobbo-Neto L,Schmidt TJ,Da Costa FB

更新日期：2015-01-26 00:00:00

abstract：:In this article, we present a systematic way to classify a family of high-genus fullerenes (HGFs) by decomposing them into two types of necklike structures, which are the negatively curved parts of parent toroidal carbon nanotubes. By replacing the faces of a uniform polyhedron with these necks, an HGF polyhedron corr...

journal_title：Journal of chemical information and modeling

authors： Chuang C,Jin BY

更新日期：2009-07-01 00:00:00

abstract：:This article presents the computation of both inter- and intramolecular hydrogen bond strengths from first-principles. Quantum chemical calculations conducted at the dispersion-corrected density functional theory level including free energy and solvation contributions are conducted for (i) one-to-one hydrogen-bonded c...

journal_title：Journal of chemical information and modeling

authors： Bauer CA

更新日期：2019-09-23 00:00:00

abstract：:Aminoglycosides are antibiotics targeting the 16S RNA A site of the bacterial ribosome. There have been many efforts directed toward design of their synthetic derivatives, however with only few successes. As RNA binders, aminoglycosides are also a difficult target for computational drug design, since most of the exist...

journal_title：Journal of chemical information and modeling

authors： Setny P,Trylska J

更新日期：2009-02-01 00:00:00

abstract：:The partitioning of solute molecules between immiscible solvents with significantly different polarities is of great importance. The polarization between the solute and solvent molecules plays an essential role in determining the solubility of the solute, which makes computational studies utilizing molecular mechanics...

journal_title：Journal of chemical information and modeling

authors： Wang M,Li P,Jia X,Liu W,Shao Y,Hu W,Zheng J,Brooks BR,Mei Y

更新日期：2017-10-23 00:00:00

abstract：:MHC class II molecules bind peptides derived from extracellular proteins that have been ingested by antigen-presenting cells and display them to the immune system. Peptide loading occurs within the antigen-presenting cell and is facilitated by HLA-DM. HLA-DM stabilizes the open conformation of the MHCII binding groove...

journal_title：Journal of chemical information and modeling

authors： Demharter S,Knapp B,Deane C,Minary P

更新日期：2019-06-24 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：:Fragment-based methods have emerged in the last two decades as alternatives to traditional high throughput screenings for the identification of chemical starting points in drug discovery. One arguable yet popular assumption about fragment-based design is that the fragment binding mode remains conserved upon chemical e...

journal_title：Journal of chemical information and modeling

authors： Bisignano P,Lambruschini C,Bicego M,Murino V,Favia AD,Cavalli A

更新日期：2012-12-21 00:00:00

abstract：:Umami or the taste of monosodium glutamate represents one of the major attractive taste modalities in humans. Therefore, knowledge about biophysical and biochemical properties of the umami taste is important for both scientific research and the food industry. Experimental approaches for predicting umami peptides are l...

journal_title：Journal of chemical information and modeling

authors： Charoenkwan P,Yana J,Nantasenamat C,Hasan MM,Shoombuatong W

更新日期：2020-12-28 00:00:00

abstract：:The importance of thorough analyses of the secondary structures in proteins as basic structural units cannot be overemphasized. Although recent computational methods have achieved reasonably high accuracy for predicting secondary structures from amino acid sequences, a simple and fundamental empirical approach to char...

journal_title：Journal of chemical information and modeling

authors： Otaki JM,Tsutsumi M,Gotoh T,Yamamoto H

更新日期：2010-04-26 00:00:00

abstract：:In this study, we tried to establish a general scheme to create a model that could predict the affinity of small compounds to their target proteins. This scheme consists of a search for ligand-binding sites on a protein, a generation of bound conformations (poses) of ligands in each of the sites by docking, identifica...

journal_title：Journal of chemical information and modeling

authors： Yasuo K,Yamaotsu N,Gouda H,Tsujishita H,Hirono S

更新日期：2009-04-01 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：:Fragment complementation is gaining an increasing impact as a nonperturbing method to probe noncovalent interactions within protein supersecondary structures. In this study, the fast Fourier transform rigid-body docking algorithm ZDOCK has been employed for in silico reconstitution of the calcium binding protein calbi...

journal_title：Journal of chemical information and modeling

authors： Dell'Orco D,Seeber M,De Benedetti PG,Fanelli F

更新日期：2005-09-01 00:00:00

abstract：:The quantitative structure-activity relationship (QSAR) approach has been used to model a wide range of chemical-induced biological responses. However, it had not been utilized to model chemical-induced genomewide gene expression changes until very recently, owing to the complexity of training and evaluating a very la...

journal_title：Journal of chemical information and modeling

authors： Liu R,AbdulHameed MDM,Wallqvist A

更新日期：2017-09-25 00:00:00

abstract：:Cyanobacterial fructose-1,6-/sedoheptulose-1,7-bisphoshatase (cy-FBP/SBPase) is a potential enzymatic target for screening of novel inhibitors that can combat harmful algal blooms. In the present study, we targeted the substrate binding pocket of cy-FBP/SBPase. A series of novel hit compounds from the SPECs database w...

journal_title：Journal of chemical information and modeling

authors： Sun Y,Zhang R,Li D,Feng L,Wu D,Feng L,Huang P,Ren Y,Feng J,Xiao S,Wan J

更新日期：2014-03-24 00:00:00

abstract：:Targeted covalent inhibitors (TCIs) have been successfully developed as high-affinity and selective inhibitors of enzymes of the protein kinase family. These drugs typically act by undergoing an electrophilic addition with an active-site cysteine residue, so design of a TCI begins with the identification of a "druggab...

journal_title：Journal of chemical information and modeling

authors： Awoonor-Williams E,Rowley CN

更新日期：2018-09-24 00:00:00

abstract：:Acetohydroxyacid synthase (AHAS) is a thiamin diphosphate-dependent enzyme involved in the biosynthesis of valine, leucine, isoleucine, and lysine. Experimental evidence has shown that mutation of the Gln202 residue results in a decrease in the enzymatic activity, thus suggesting the main role of the carboligation cat...

journal_title：Journal of chemical information and modeling

authors： Mendoza F,Medina FE,Jiménez VA,Jaña GA

更新日期：2020-02-24 00:00:00

abstract：:We demonstrate that using an all-atom molecular mechanics force field combined with an implicit solvent model for scoring protein-ligand complexes is a promising approach for improving inhibitor enrichment in the virtual screening of large compound databases. The rescoring method is evaluated by the extent to which kn...

journal_title：Journal of chemical information and modeling

authors： Huang N,Kalyanaraman C,Irwin JJ,Jacobson MP

更新日期：2006-01-01 00:00:00