From Brazil to Germany: Challenges and Advantages.

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：:Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics and biological research. The charge migration rate is controlled by the electronic couplings between the two nucleobases of DNA/RNA. These electronic coupling...

journal_title：Journal of chemical information and modeling

authors： Aggarwal A,Vinayak V,Bag S,Bhattacharyya C,Waghmare UV,Maiti PK

更新日期：2021-01-25 00:00:00

abstract：:The metabolism of xenobiotics--and more specifically drugs--in the liver is a critical process controlling their half-life. Although there exist experimental methods, which measure the metabolic stability of xenobiotics and identify their metabolites, developing higher throughput predictive methods is an avenue of res...

journal_title：Journal of chemical information and modeling

authors： Campagna-Slater V,Pottel J,Therrien E,Cantin LD,Moitessier N

更新日期：2012-09-24 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：:Partial covalent interactions (PCIs) in proteins, which include hydrogen bonds, salt bridges, cation-π, and π-π interactions, contribute to thermodynamic stability and facilitate interactions with other biomolecules. Several score functions have been developed within the Rosetta protein modeling framework that identif...

journal_title：Journal of chemical information and modeling

authors： Combs SA,Mueller BK,Meiler J

更新日期：2018-05-29 00:00:00

abstract：:The ONIOM scheme is one of the most popular QM/MM approaches, but its extended application has been so far hindered by the limited availability of force fields in most practical implementations. This paper describes a simple software code to overcome this limitation, and its application to three representative chemica...

journal_title：Journal of chemical information and modeling

authors： Sameera WMC,Maseras F

更新日期：2018-09-24 00:00:00

abstract：:Small molecule flexible alignment is a critical component of both ligand- and structure-based methods in computer-aided drug discovery. Despite its importance, the availability of high-quality flexible alignment software packages is limited. Here, we present BCL::MolAlign, a freely available property-based molecular a...

journal_title：Journal of chemical information and modeling

authors： Brown BP,Mendenhall J,Meiler J

更新日期：2019-02-25 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：:Many of the conventional similarity methods assume that molecular fragments that do not relate to biological activity carry the same weight as the important ones. One possible approach to this problem is to use the Bayesian inference network (BIN), which models molecules and reference structures as probabilistic infer...

journal_title：Journal of chemical information and modeling

authors： Abdo A,Salim N

更新日期：2011-01-24 00:00:00

abstract：:Due to the importance of hot-spots (HS) detection and the efficiency of computational methodologies, several HS detecting approaches have been developed. The current paper presents new models to predict HS for protein-protein and protein-nucleic acid interactions with better statistics compared with the ones currently...

journal_title：Journal of chemical information and modeling

authors： Munteanu CR,Pimenta AC,Fernandez-Lozano C,Melo A,Cordeiro MN,Moreira IS

更新日期：2015-05-26 00:00:00

abstract：:Searching chemical databases for possible drug leads is often one of the main activities conducted during the early stages of a drug development project. This article shows that spherical harmonic molecular shape representations provide a powerful way to search and cluster small-molecule databases rapidly and accurate...

journal_title：Journal of chemical information and modeling

authors： Mavridis L,Hudson BD,Ritchie DW

更新日期：2007-09-01 00:00:00

abstract：:The important role of water molecules in protein-ligand binding energetics has attracted wide attention in recent years. A range of computational methods has been developed to predict the favorable locations of water molecules in a protein binding pocket. Most of the current methods are based on extensive molecular dy...

journal_title：Journal of chemical information and modeling

authors： Li Y,Gao Y,Holloway MK,Wang R

更新日期：2020-09-28 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：:G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors, which is arguably the most important family of drug target. With the technology breakthroughs in X-ray crystallography and cryo-electron microscopy, more than 300 GPCR-ligand complex structures have been publicly reported since 2007,...

journal_title：Journal of chemical information and modeling

authors： Li Y,Sun Y,Song Y,Dai D,Zhao Z,Zhang Q,Zhong W,Hu LA,Ma Y,Li X,Wang R

更新日期：2020-09-28 00:00:00

abstract：:Retrieving molecules with specific structural features is a fundamental requirement of today's molecular database technologies. Estimates claim the chemical space relevant for drug discovery to be around 10⁶⁰ molecules. This figure is many orders of magnitude larger than the amount of molecules conventional databases ...

journal_title：Journal of chemical information and modeling

authors： Ehrlich HC,Henzler AM,Rarey M

更新日期：2013-07-22 00:00:00

abstract：:It is of great interest in modern drug design to accurately calculate the free energies of protein-ligand or nucleic acid-ligand binding. MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) and MM-GBSA (molecular mechanics generalized Born surface area) have gained popularity in this field. For both methods, ...

journal_title：Journal of chemical information and modeling

authors： Wang J,Hou T

更新日期：2012-05-25 00:00:00

abstract：:The COSMO surface polarization charge density σ resulting from quantum chemical calculations combined with a virtual conductor embedding has been widely proven to be a very suitable descriptor for the quantification of interactions of molecules in liquids. In a preceding paper, grid-based local histograms of σ have be...

journal_title：Journal of chemical information and modeling

authors： Klamt A,Thormann M,Wichmann K,Tosco P

更新日期：2012-08-27 00:00:00

abstract：:FFAR4 has been considered as a potential target for metabolic diseases, including diabetes. Some compounds with biphenyl scaffold, represented by compound SR13 reported by our group, showed significant FFAR4 selectivity. However, the molecular basis for their selectivity has not been definitely disclosed. This study p...

journal_title：Journal of chemical information and modeling

authors： Zhang X,Sun H,Wen X,Yuan H

更新日期：2019-10-28 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：:We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables ...

journal_title：Journal of chemical information and modeling

authors： Borstnik U,Janezic D

更新日期：2005-11-01 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：:Generalization of an earlier algorithm has led to the development of new local structural alignment algorithms for prediction of protein-protein binding sites. The algorithms use maximum cliques on protein graphs to define structurally similar protein regions. The search for structural neighbors in the new algorithms ...

journal_title：Journal of chemical information and modeling

authors： Carl N,Konc J,Vehar B,Janezic D

更新日期：2010-10-25 00:00:00

abstract：:The sensitivity of docking calculations to the geometry of the input ligand was studied. It was found that even small changes in the ligand input conformation can lead to large differences in the geometries and scores of the resulting docked poses. The accuracy of docked poses produced from different ligand input stru...

journal_title：Journal of chemical information and modeling

authors： Feher M,Williams CI

更新日期：2009-07-01 00:00:00

abstract：:Ergotamine (ERG) and dihydroergotamine (DHE), common migraine drugs, have small structural differences but lead to clinically important distinctions in their pharmacological profiles. For example, DHE is less potent than ERG by about 10-fold at the 5-hydroxytrptamine receptor 1B (5-HT1B). Although the high-resolution ...

journal_title：Journal of chemical information and modeling

authors： Sullivan HJ,Tursi A,Moore K,Campbell A,Floyd C,Wu C

更新日期：2020-03-23 00:00:00

abstract：:Among the photophysical parameters that underpin Förster resonance energy transfer (FRET), perhaps the least explored is the spectral overlap term ( J). While by definition J increases linearly with acceptor molar absorption coefficient (ε(A) in M-1 cm-1), is proportional to wavelength (λ4), and depends on the degree ...

journal_title：Journal of chemical information and modeling

authors： Qi Q,Taniguchi M,Lindsey JS

更新日期：2019-02-25 00:00:00

abstract：:The hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRP) is a crucial and unique component of the HCV RNA replication machinery and a validated target for drug discovery. Multiple crystal structures of NS5B inhibitor complexes have facilitated the identification of novel compound scaffolds through in silic...

journal_title：Journal of chemical information and modeling

authors： Therese PJ,Manvar D,Kondepudi S,Battu MB,Sriram D,Basu A,Yogeeswari P,Kaushik-Basu N

更新日期：2014-02-24 00:00:00

abstract：:Identifying drug-target interactions (DTIs) plays an important role in the field of drug discovery, drug side-effects, and drug repositioning. However, in vivo or biochemical experimental methods for identifying new DTIs are extremely expensive and time-consuming. Recently, in silico or various computational methods h...

journal_title：Journal of chemical information and modeling

authors： Xia LY,Yang ZY,Zhang H,Liang Y

更新日期：2019-07-22 00:00:00

abstract：:The industrial production of higher-generation semisynthetic cephalosporins starts from 7-aminocephalosporanic acid (7-ACA), which is obtained by deacylation of the naturally occurring antibiotic cephalosporin C (CephC). The enzymatic process in which CephC is directly converted into 7-ACA by a cephalosporin C acylase...

journal_title：Journal of chemical information and modeling

authors： Mollica L,Conti G,Pollegioni L,Cavalli A,Rosini E

更新日期：2015-10-26 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：:CYP19A1, also known as aromatase or estrogen synthetase, is the rate-limiting enzyme in the biosynthesis of estrogens from their corresponding androgens. Several clinically used breast cancer therapies target aromatase. In this work, explicitly solvated all-atom molecular dynamics simulations of aromatase with a model...

journal_title：Journal of chemical information and modeling

authors： Park J,Czapla L,Amaro RE

更新日期：2013-08-26 00:00:00