Facile Solutions to the Problems Associated with Chemical Information and Mathematical Symbolism While Using Machine Translation Tools.

abstract：:Throughout the drug discovery process, discovery teams are compelled to use statistics for making decisions using data from a variety of inputs. For instance, teams are asked to prioritize compounds for subsequent stages of the drug discovery process, given results from multiple screens. To assist in the prioritizatio...

journal_title：Journal of chemical information and modeling

authors： Mandal A,Johnson K,Wu CF,Bornemeier D

更新日期：2007-05-01 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：:Protein-polysaccharide complexes constructed via self-assembly methods are often used to develop novel biomaterials for a wide range of applications in biomedicine, food, and biotechnology. The objective of this work was to investigate theoretically and to demonstrate via constant-pH Monte Carlo simulations that the c...

journal_title：Journal of chemical information and modeling

authors： Prudkin-Silva C,Pérez OE,Martínez KD,Barroso da Silva FL

更新日期：2020-02-24 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：: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：:We report the synthesis and a study of the structure-activity relationships of a new series of diarylhydrazides as potential selective non-ligand binding pocket androgen receptor antagonists. Their biological activity as antiandrogens in the context of the development of treatments for castration resistant prostate ca...

journal_title：Journal of chemical information and modeling

authors： Caboni L,Egan B,Kelly B,Blanco F,Fayne D,Meegan MJ,Lloyd DG

更新日期：2013-08-26 00:00:00

abstract：:Scoring the activity of compounds in phenotypic high-throughput assays presents a unique challenge because of the limited resolution and inherent measurement error of these assays. Techniques that leverage the structural similarity of compounds within an assay can be used to improve the hit-recovery rate from screenin...

journal_title：Journal of chemical information and modeling

authors： Klekota J,Brauner E,Schreiber SL

更新日期：2005-11-01 00:00:00

abstract：:Binding hot spots are regions of proteins that, due to their potentially high contribution to the binding free energy, have high propensity to bind small molecules. We present benchmark sets for testing computational methods for the identification of binding hot spots with emphasis on fragment-based ligand discovery. ...

journal_title：Journal of chemical information and modeling

authors： Wakefield AE,Yueh C,Beglov D,Castilho MS,Kozakov D,Keserű GM,Whitty A,Vajda S

更新日期：2020-12-28 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 phenotypic screen (PS) is used to identify compounds causing a desired phenotype in a complex biological system where mechanisms and targets are largely unknown. Deconvoluting the mechanism of action of actives and identification of relevant targets and pathways remains a formidable challenge. Current methods fail t...

journal_title：Journal of chemical information and modeling

authors： Polyakov VR,Moorcroft ND,Drawid A

更新日期：2014-02-24 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：:DNA damage alters genetic information and adversely affects gene expression pathways leading to various complex genetic disorders and cancers. DNA repair proteins recognize and rectify DNA damage and mismatches with high fidelity. A critical molecular event that occurs during most protein-mediated DNA repair processes...

journal_title：Journal of chemical information and modeling

authors： Pitta K,Krishnan M

更新日期：2018-03-26 00:00:00

abstract：:Given the essential role played by protein kinases in regulating cellular pathways, their dysregulation can result in the onset and/or progression of various human diseases. Structural analysis of diverse protein kinases suggests that these proteins exhibit a remarkable plasticity that allows them to adopt distinct co...

journal_title：Journal of chemical information and modeling

authors： Gomez-Gutierrez P,Rubio-Martinez J,Perez JJ

更新日期：2017-10-23 00:00:00

abstract：:The early stages of drug discovery rely on hit-to-lead programs, where initial hits undergo partial optimization to improve binding affinities for their biological target. This is an expensive and time-consuming process, requiring multiple iterations of trial and error designs, an ideal scenario for applying computer ...

journal_title：Journal of chemical information and modeling

authors： Perez C,Soler D,Soliva R,Guallar V

更新日期：2020-03-23 00:00:00

abstract：:3-Pyridyl ethers are excellent nAChRs ligands, which show high subtype selectivity and binding affinity to alpha4beta2 nAChR. Although the quantitative structure-activity relationship (QSAR) of nAChRs ligands has been widely investigated using various classes of compounds, the open ring analogues of 3-pyridyl ethers h...

journal_title：Journal of chemical information and modeling

authors： Zhang H,Li H,Liu C

更新日期：2005-03-01 00:00:00

abstract：:Spin diffusion is a formidable problem when interpreting NMR data of chemical compounds. We developed a method to reconstruct the conformational ensemble of flexible molecules displaying spin diffusion, which minimizes the subjective bias in the interpretation of experimental data and which can be used routinely to ob...

journal_title：Journal of chemical information and modeling

authors： Vasile F,Tiana G

更新日期：2019-06-24 00:00:00

abstract：:Flavonoids, the vastest class of natural polyphenols, are extensively investigated for their multiple benefits on human health. Due to their physicochemical or biological properties, many representatives are considered to exhibit low selectivity among various protein targets or to plague high-throughput screening (HTS...

journal_title：Journal of chemical information and modeling

authors： Avram SI,Pacureanu LM,Bora A,Crisan L,Avram S,Kurunczi L

更新日期：2014-08-25 00:00:00

abstract：:Inhibition of plasmin has been found to effectively reduce fibrinolysis and to avoid hemorrhage. This can be achieved by addressing its kringle 1 domain with the known drug and lysine analogue tranexamic acid. Guided by shape similarities toward a previously discovered lead compound, 5-(4-piperidyl)isoxazol-3-ol, a se...

journal_title：Journal of chemical information and modeling

authors： Schmidt TC,Eriksson PO,Gustafsson D,Cosgrove D,Frølund B,Boström J

更新日期：2017-07-24 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：: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 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：:The efficiency of automated compound screening is heavily influenced by the design and the quality of the screening libraries used. We recently reported on the assembly of one diverse and one target-focused lead-like screening library. Using data from 15 enzyme-based screenings conducted using these libraries, their p...

journal_title：Journal of chemical information and modeling

authors： Mok NY,Maxe S,Brenk R

更新日期：2013-03-25 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：: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：:Rotational Profiler provides an analytical algorithm to compute sets of classical torsional dihedral parameters by fitting an empirical energy profile to a reference one that can be obtained experimentally or by quantum-mechanical methods. The resulting profiles are compatible with the functional forms in the most wid...

journal_title：Journal of chemical information and modeling

authors： Rusu VH,Santos DES,Poleto MD,Galheigo MM,Gomes ATA,Verli H,Soares TA,Lins RD

更新日期：2020-12-28 00:00:00

abstract：:The large volume of protein-ligand structures now available enables innovative and efficient protocols in computational FBDD (Fragment-Based Drug Design) to be proposed based on experimental data. In this work, we build a database of MED-Portions, where a MED-Portion is a new structural object encoding protein-fragmen...

journal_title：Journal of chemical information and modeling

authors： Moriaud F,Doppelt-Azeroual O,Martin L,Oguievetskaia K,Koch K,Vorotyntsev A,Adcock SA,Delfaud F

更新日期：2009-02-01 00:00:00

abstract：:Sterol 14α-demethylase (CYP51) is the main drug target for the treatment of fungal infections. The discovery of new efficient fungal CYP51 inhibitors requires an understanding of the structural requirements for selectivity for the fungal over the human ortholog. In this study, a binding mode of the pyridylethanol(phen...

journal_title：Journal of chemical information and modeling

authors： Zelenko U,Hodošček M,Rozman D,Golič Grdadolnik S

更新日期：2014-12-22 00:00:00

abstract：:This work is aimed at describing the workflow for a methodology that combines chemoinformatics and pharmacoepidemiology methods and at reporting the first predictive model developed with this methodology. The new model is able to predict complex networks of AIDS prevalence in the US counties, taking into consideration...

journal_title：Journal of chemical information and modeling

authors： González-Díaz H,Herrera-Ibatá DM,Duardo-Sánchez A,Munteanu CR,Orbegozo-Medina RA,Pazos A

更新日期：2014-03-24 00:00:00

abstract：:We introduce SARANEA, an open-source Java application for interactive exploration of structure-activity relationship (SAR) and structure-selectivity relationship (SSR) information in compound sets of any source. SARANEA integrates various SAR and SSR analysis functions and utilizes a network-like similarity graph data...

journal_title：Journal of chemical information and modeling

authors： Lounkine E,Wawer M,Wassermann AM,Bajorath J

更新日期：2010-01-01 00:00:00

abstract：:The similarity/diversity measures play a fundamental role in library searching, virtual screening, and quantitative structure-activity relationship/quantitative structure-property relationship modeling as well as in genomics and proteomics. In this paper, a new similarity/diversity measure is proposed as a new approac...

journal_title：Journal of chemical information and modeling

authors： Todeschini R,Consonni V,Mauri A,Ballabio D

更新日期：2006-09-01 00:00:00