Pharmacophore model for bile acids recognition by the FPR receptor.

abstract：:Computational techniques, such as Quantitative Structure-Property Relationship (QSPR) modeling, are very useful in predicting physicochemical properties of various chemicals. Building QSPR models requires calculating molecular descriptors and the proper choice of the geometry optimization method, which will be dedicat...

journal_title：Journal of computer-aided molecular design

authors： Rybinska A,Sosnowska A,Barycki M,Puzyn T

更新日期：2016-02-01 00:00:00

abstract：:Chemical libraries contain thousands of compounds that need screening, which increases the need for computational methods that can rank or prioritize compounds. The tools of virtual screening are widely exploited to enhance the cost effectiveness of lead drug discovery programs by ranking chemical compounds databases ...

journal_title：Journal of computer-aided molecular design

authors： Al-Dabbagh MM,Salim N,Himmat M,Ahmed A,Saeed F

更新日期：2017-04-01 00:00:00

abstract：:Thirty-six compounds, representing six different structural classes of insecticides which are known to act at the gamma-aminobutyric acid receptor/chloride ionophore, have been superimposed by methods which maximise the commonality of steric and electrostatic fields. Maximal steric and electrostatic alignment was deri...

journal_title：Journal of computer-aided molecular design

authors： Calder JA,Wyatt JA,Frenkel DA,Casida JE

更新日期：1993-02-01 00:00:00

abstract：:Crystal structures of the 1,4-dihydropyridine (1,4-DHP) calcium channel activators Bay K 8643 [methyl 1,4-dihydro-2,6-dimethyl-3-nitro-4-(3-nitrophenyl)-pyridine-5-carboxy lat e], Bay O 8495 [methyl 1,4-dihydro-2,6-dimethyl-3-nitro-4-(3-trifluoromethylphenyl)-pyridine-5- carboxylate], and Bay O 9507 [methyl 1,4-dihydr...

journal_title：Journal of computer-aided molecular design

authors： Langs DA,Kwon YW,Strong PD,Triggle DJ

更新日期：1991-04-01 00:00:00

abstract：:We apply an atomistic model of passive membrane permeability to a series of weakly basic drugs. The computational model uses conformational sampling in combination with an all-atom force field and implicit solvent model to estimate relative passive membrane permeabilities. The model does not require the use of trainin...

journal_title：Journal of computer-aided molecular design

authors： Kalyanaraman C,Jacobson MP

更新日期：2007-12-01 00:00:00

abstract：:Macroscopic pKa values were calculated for all compounds in the SAMPL6 blind prediction challenge, based on quantum chemical calculations with a continuum solvation model and a linear correction derived from a small training set. Microscopic pKa values were derived from the gas-phase free energy difference between pro...

journal_title：Journal of computer-aided molecular design

authors： Selwa E,Kenney IM,Beckstein O,Iorga BI

更新日期：2018-10-01 00:00:00

abstract：:An analysis of five different datasets of inhibitors of serotonin uptake has yielded quantitative structure/activity relationships (QSARs) which delineate the role of steric and hydrophobic properties essential for inhibition by phenylethylamine-type analogues. ...

journal_title：Journal of computer-aided molecular design

authors： Hansch C,Caldwell J

更新日期：1991-10-01 00:00:00

abstract：:The growing number of protein-ligand complex structures, particularly the structures of proteins co-bound with different ligands, in the Protein Data Bank helps us tackle two major challenges in molecular docking studies: the protein flexibility and the scoring function. Here, we introduced a systematic strategy by us...

journal_title：Journal of computer-aided molecular design

authors： Xu X,Yan C,Zou X

更新日期：2017-08-01 00:00:00

abstract：:Moment descriptors of the molecular charge and mass distributions are investigated within the context of molecular similarity. Euclidean distances in the moment descriptor space are shown to yield molecular proximities in accord with chemical intuition for a substituted [(4-phenylpiperazinyl)-methyl] benzamide series ...

journal_title：Journal of computer-aided molecular design

authors： Silverman BD,Pitman MC,Platt DE,Rigoutsos I

更新日期：1998-11-01 00:00:00

abstract：:We developed a new structure-based in-silico screening method using a negative image of a ligand-binding pocket and a multi-protein-compound interaction matrix. Based on the structure of the ligand pocket of the target protein, we designed a negative image, which consists of virtual atoms whose radii are close to thos...

journal_title：Journal of computer-aided molecular design

authors： Fukunishi Y,Kubota S,Kanai C,Nakamura H

更新日期：2006-04-01 00:00:00

abstract：:The Drug Design Data Resource (D3R) Grand Challenges present an opportunity to assess, in the context of a blind predictive challenge, the accuracy and the limits of tools and methodologies designed to help guide pharmaceutical drug discovery projects. Here, we report the results of our participation in the D3R Grand ...

journal_title：Journal of computer-aided molecular design

authors： Sasmal S,El Khoury L,Mobley DL

更新日期：2020-02-01 00:00:00

abstract：:The Fas antigen, a cell surface receptor belonging to the tumor necrosis factor receptor (TNFR) superfamily, triggers programmed cell death (apoptosis) in the immune system. The three-dimensional structure of Fas and molecular details of the interaction between Fas and its ligand are currently unknown. A three-dimensi...

journal_title：Journal of computer-aided molecular design

authors： Bajorath J,Aruffo A

更新日期：1997-01-01 00:00:00

abstract：:One of the most important pharmacological mechanisms of antimalarial action is the inhibition of the aggregation of hematin into hemozoin. We present a group of new potential antimalarial molecules for which we have performed a DFT study of their stereoelectronic properties. Additionally, the same calculations were ca...

journal_title：Journal of computer-aided molecular design

authors： Portela C,Afonso CM,Pinto MM,Ramos MJ

更新日期：2003-09-01 00:00:00

abstract：:Capacity ratio (log k') values, which are a measure of hydrophobicity, were calculated directly from the three-dimensional structures of 17 furans and 54 triazines using the comparative molecular field analysis approach. The H2O probe and the GRID force field, including hydrogen-bond potentials, yielded excellent corr...

journal_title：Journal of computer-aided molecular design

authors： Kim KH

更新日期：1995-08-01 00:00:00

abstract：:In previous studies we have developed categorical QSAR models for predicting skin-sensitization potency based on 4D-fingerprint (4D-FP) descriptors and in vivo murine local lymph node assay (LLNA) measures. Only 4D-FP derived from the ground state (GMAX) structures of the molecules were used to build the QSAR models. ...

journal_title：Journal of computer-aided molecular design

authors： Liu J,Kern PS,Gerberick GF,Santos-Filho OA,Esposito EX,Hopfinger AJ,Tseng YJ

更新日期：2008-06-01 00:00:00

abstract：:The liver is extremely vulnerable to the effects of xenobiotics due to its critical role in metabolism. Drug-induced hepatotoxicity may involve any number of different liver injuries, some of which lead to organ failure and, ultimately, patient death. Understandably, liver toxicity is one of the most important dose-li...

journal_title：Journal of computer-aided molecular design

authors： Cheng A,Dixon SL

更新日期：2003-12-01 00:00:00

abstract：:Molecular structures and functions of the majority of proteins across different species are yet to be identified. Much needed functional annotation of these gene products often benefits from the knowledge of protein-ligand interactions. Towards this goal, we developed eFindSite, an improved version of FINDSITE, design...

journal_title：Journal of computer-aided molecular design

authors： Brylinski M,Feinstein WP

更新日期：2013-06-01 00:00:00

abstract：:Intercalative binding of the antitumor drugs amonafide and azonafide to the oligonucleotide duplex d(GGCCGGCCGG).d(CCGGCCGGCC) was compared using molecular dynamics in vacuum with the AMBER force field. A number of reasonable possible binding conformations were obtained, with the azonafide complexes favored over the a...

journal_title：Journal of computer-aided molecular design

authors： Bear S,Remers WA

更新日期：1996-04-01 00:00:00

abstract：:The process of compound selection and prioritization is crucial for both combinatorial chemistry (CBC) and high throughput screening (HTS). Compound libraries have to be screened for unwanted chemical structures, as well as for unwanted chemical properties. Property extrema can be eliminated by using property filters,...

journal_title：Journal of computer-aided molecular design

authors： Oprea TI

更新日期：2000-03-01 00:00:00

abstract：:The binding properties of sequence-specific nucleic acids (aptamers) to low-molecular-weight ligands, macromolecules and even cells attract substantial scientific interest. These ligand-DNA complexes found different applications for sensing, nanomedicine, and DNA nanotechnology. Structural information on the aptamer-l...

journal_title：Journal of computer-aided molecular design

authors： Albada HB,Golub E,Willner I

更新日期：2015-07-01 00:00:00

abstract：:This paper tests the performance of a simple empirical scoring function on a set of candidate designs produced by a de novo design package. The scoring function calculates approximate ligand-receptor binding affinities given a putative binding geometry. To our knowledge this is the first substantial test of an empiric...

journal_title：Journal of computer-aided molecular design

authors： Murray CW,Auton TR,Eldridge MD

更新日期：1998-09-01 00:00:00

abstract：:A quantitative analysis of the interaction sites of the anti-Alzheimer drug galanthamine with molecular probes (water and benzene molecules) representative of its surroundings in the binding site of acetylcholinesterase (AChE) has been realized through pairwise potentials calculations and quantum chemistry. This strat...

journal_title：Journal of computer-aided molecular design

authors： Galland N,Kone S,Le Questel JY

更新日期：2012-10-01 00:00:00

abstract：:A three-dimensional quantitative spectrometric data-activity relationship (3D-QSDAR) modeling technique which uses NMR spectral and structural information that is combined in a 3D-connectivity matrix has been developed. A 3D-connectivity matrix was built by displaying all possible assigned carbon NMR chemical shifts, ...

journal_title：Journal of computer-aided molecular design

authors： Beger RD,Buzatu DA,Wilkes JG

更新日期：2002-10-01 00:00:00

abstract：:During the last few years, we have developed a docking protocol involving two steps: (i) the choice of the most appropriate docking software and parameters for the system of interest using structural and functional information available in public databases (PDB, ChEMBL, PubChem Assay, BindingDB, etc.); (ii) the dockin...

journal_title：Journal of computer-aided molecular design

authors： Chaput L,Selwa E,Elisée E,Iorga BI

更新日期：2019-01-01 00:00:00

abstract：:In the 1960s, the kappa statistic was introduced for the estimation of chance agreement in inter- and intra-rater reliability studies. The kappa statistic was strongly pushed by the medical field where it could be successfully applied via analyzing diagnoses of identical patient groups. Kappa is well suited for classi...

journal_title：Journal of computer-aided molecular design

authors： Czodrowski P

更新日期：2014-11-01 00:00:00

abstract：:Drug discovery is an expensive and time-consuming process. To make this process more efficient quantum chemistry methods can be employed. The electrophilicity index is one property that can be calculated by quantum chemistry methods, and if calculated correctly gives insight into the reactivity of covalent inhibitors....

journal_title：Journal of computer-aided molecular design

authors： Hermann MR,Pautsch A,Grundl MA,Weber A,Tautermann CS

更新日期：2020-10-05 00:00:00

abstract：:Overexpression of Bcl-2 and Bcl-xL proteins, both inhibitors of apoptosis or programmed cell death, is related to the generation and development of several types of cancer as well as to an elevated resistance to chemotherapeutic treatments. Given that synthetic peptide fragments of the BH3 domain are capable to bind t...

journal_title：Journal of computer-aided molecular design

authors： Pinto M,Perez JJ,Rubio-Martinez J

更新日期：2004-01-01 00:00:00

abstract：:We have undertaken molecular dynamics simulations on the d(CGCAAAAAAGCG).d(CGCTTTTTTGCG) dodecamer in solution. In this study, we focus on aspects of conformation and dynamics, including the possibility of cross-strand hydrogen bonds. We compare our results with those from crystallography as well as infrared, Raman an...

journal_title：Journal of computer-aided molecular design

authors： de Souza ON,Goodfellow JM

更新日期：1994-06-01 00:00:00

abstract：:Learning strategies can be used to improve the efficiency of virtual screening of very large databases. In these strategies new compounds to be screened are selected on the basis of the results obtained in previous stages, even if truly good ligands have not yet been identified. This approach requires that the scoring...

journal_title：Journal of computer-aided molecular design

authors： Cincilla G,Vidal D,Pons M

更新日期：2009-03-01 00:00:00

abstract：:The mounting evidences have shown that signal transducer and activator of transcription 3 (Stat3) is a critical target for cancer therapy. Recently, we developed a G-quartet oligonucleotide T40214 as a novel and potent Stat3 inhibitor. T40214 specifically inhibited DNA-binding activity of Stat3 and significantly suppr...

journal_title：Journal of computer-aided molecular design

authors： Zhu Q,Jing N

更新日期：2007-10-01 00:00:00