Antimalarial activity of synthetic 1,2,4-trioxanes and cyclic peroxy ketals, a quantum similarity study.

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：:Evidenced by the three-rounds of G-protein coupled receptors (GPCR) Dock competitions, improving homology modeling methods of helical transmembrane proteins including the GPCRs, based on templates of low sequence identity, remains an eminent challenge. Current approaches addressing this challenge adopt the philosophy ...

journal_title：Journal of computer-aided molecular design

authors： Chaudhari R,Heim AJ,Li Z

更新日期：2015-05-01 00:00:00

abstract：:New designs for Magnetic Resonance Imaging contrast agents are presented. Essentially, they all are host-guest inclusion complexes between y-cyclodextrins and polyazamacrocycles of gadolinium (III) ion. Substitutions have been made to the host to optimise the host-guest association. Molecular mechanics calculations ha...

journal_title：Journal of computer-aided molecular design

authors： Fernandes PA,Carvalho AT,Marques AT,Pereira AL,Madeira AP,Ribeiro AS,Carvalho AF,Ricardo ET,Pinto FJ,Santos HA,Mangericão HD,Martins HM,Pinto HD,Santos HR,Moreira IS,Azeredo MJ,Abreu RP,Oliveira RM,Sousa SF,Silva RJ

更新日期：2003-07-01 00:00:00

abstract：:Glucokinase (GK) is involved in normal glucose homeostasis and therefore it is a valid target for drug design and discovery efforts. GK activators (GKAs) have excellent potential as treatments of hyperglycemia and diabetes. The combined recent interest in GKAs, together with docking limitations and shortages of dockin...

journal_title：Journal of computer-aided molecular design

authors： Taha MO,Habash M,Khanfar MA

更新日期：2014-05-01 00:00:00

abstract：:The pKa is the standard measure used to describe the aqueous proton affinity of a compound, indicating the proton concentration (pH) at which two protonation states (e.g. A- and AH) have equal free energy. However, compounds can have additional protonation states (e.g. AH2+), and may assume multiple tautomeric forms, ...

journal_title：Journal of computer-aided molecular design

authors： Gunner MR,Murakami T,Rustenburg AS,Işık M,Chodera JD

更新日期：2020-05-01 00:00:00

abstract：:Targeting Proviral integration-site of murine Moloney leukemia virus 1 kinase, hereafter called Pim-1 kinase, is a promising strategy for treating different kinds of human cancer. Headed for this a total list of 328 formerly reported Pim-1 kinase inhibitors has been explored and divided based on the pharmacophoric fea...

journal_title：Journal of computer-aided molecular design

authors： Shahin R,Swellmeen L,Shaheen O,Aboalhaija N,Habash M

更新日期：2016-01-01 00:00:00

abstract：:The one-dimensional model of Hann et al. (JChem Inf Comput Sci 41(3):856–864) has been extended to include reverse binding and wrap-around interaction modes between the protein and ligand to explore the complete combinatorial matrix of molecular recognition. The cumulative distribution function of the Maxwell–Boltzman...

journal_title：Journal of computer-aided molecular design

authors： Nilar SH,Ma NL,Keller TH

更新日期：2013-09-01 00:00:00

abstract：:A series of non-peptide angiotensin II receptor antagonists was investigated with the aim of developing a 3D QSAR model using comparative molecular field analysis descriptors and approaches. The main goals of the study were dictated by an interest in methodologies and an understanding of the binding requirements to th...

journal_title：Journal of computer-aided molecular design

authors： Belvisi L,Bravi G,Catalano G,Mabilia M,Salimbeni A,Scolastico C

更新日期：1996-12-01 00:00:00

abstract：:Folate receptor α (FRα) is a cell surface, glycophosphatidylinositol-anchored protein which has focussed attention as a therapeutic target and as a marker for the diagnosis of cancer. It has a high affinity for the dietary supplemented folic acid (FOL), carrying out endocytic transport across the cell membrane and del...

journal_title：Journal of computer-aided molecular design

authors： Della-Longa S,Arcovito A

更新日期：2015-01-01 00:00:00

abstract：:Multipoint interactions between synthetic and natural polymers provide a promising platform for many topical applications, including therapeutic blockage of virus-specific targets. Docking may become a useful tool for modelling of such interactions. However, the rigid docking cannot be correctly applied to synthetic p...

journal_title：Journal of computer-aided molecular design

authors： Tsvetkov VB,Serbin AV

更新日期：2012-12-01 00:00:00

abstract：:Many commercially available software programs claim similar efficiency and accuracy as variable selection tools. Genetic algorithms are commonly used variable selection methods where most relevant variables can be differentiated from 'less important' variables using evolutionary computing techniques. However, differen...

journal_title：Journal of computer-aided molecular design

authors： Schefzick S,Bradley M

更新日期：2004-07-01 00:00:00

abstract：:Utilization of coupling constants as restraints in computational structure refinement is reviewed. In addition, we address the effect of conformational averaging and examine different approaches to apply the restraints when the experimental observable is obviously a result of averaging. Here, two different computation...

journal_title：Journal of computer-aided molecular design

authors： Mierke DF,Huber T,Kessler H

更新日期：1994-02-01 00:00:00

abstract：:To rigorously assess the tools and protocols that can be used to understand and predict macromolecular recognition, and to gain more structural insight into three newly discovered allosteric binding sites on a critical drug target involved in the treatment of HIV infections, the Olson and Levy labs collaborated on the...

journal_title：Journal of computer-aided molecular design

authors： Perryman AL,Santiago DN,Forli S,Martins DS,Olson AJ

更新日期：2014-04-01 00:00:00

abstract：:A theoretical conformational study was performed on leu-enkephalin in its zwitterionic form, both in vacuo and in the presence of a number, n, of up to 13 water molecules saturating its first hydration shell. The intramolecular energy of enkephalin as well as the intermolecular enkephalin-water and water-water interac...

journal_title：Journal of computer-aided molecular design

authors： Demetropoulos IN,Gresh N

更新日期：1991-04-01 00:00:00

abstract：:The overexpression and/or mutation of the epidermal growth factor receptor (EGFR) tyrosine kinase has been observed in many human solid tumors, and is under intense investigation as a novel anticancer molecular target. Comparative 3D-QSAR analyses using different alignments were undertaken employing comparative molecu...

journal_title：Journal of computer-aided molecular design

authors： Assefa H,Kamath S,Buolamwini JK

更新日期：2003-08-01 00:00:00

abstract：:The V2 vasopressin renal receptor (V2R), which controls antidiuresis in mammals, is a member of the large family of heptahelical transmembrane (7TM) G protein-coupled receptors (GPCRs). Using the automated GPCR modeling facility available via Internet (http:/(/)expasy.hcuge.ch/swissmod/SWISS-MODEL.+ ++html) for constr...

journal_title：Journal of computer-aided molecular design

authors： Czaplewski C,Kaźmierkiewicz R,Ciarkowski J

更新日期：1998-05-01 00:00:00

abstract：:In the absence of a 3D structure of the target biomolecule, to propose the 3D requirements for a small molecule to exhibit a particular bioactivity, one must supply both a bioactive conformation and a superposition rule for every active compound. Our strategy identifies both simultaneously. We first generate and optim...

journal_title：Journal of computer-aided molecular design

authors： Martin YC,Bures MG,Danaher EA,DeLazzer J,Lico I,Pavlik PA

更新日期：1993-02-01 00:00:00

abstract：:The Drug Design Data Resource (D3R) ran Grand Challenge 2015 between September 2015 and February 2016. Two targets served as the framework to test community docking and scoring methods: (1) HSP90, donated by AbbVie and the Community Structure Activity Resource (CSAR), and (2) MAP4K4, donated by Genentech. The challeng...

journal_title：Journal of computer-aided molecular design

authors： Gathiaka S,Liu S,Chiu M,Yang H,Stuckey JA,Kang YN,Delproposto J,Kubish G,Dunbar JB Jr,Carlson HA,Burley SK,Walters WP,Amaro RE,Feher VA,Gilson MK

更新日期：2016-09-01 00:00:00

abstract：:4-(Phenylamino)-pyrrolo[2,1-f][1,2,4]triazines have been discovered as inhibitors of p38alpha. Experimental assays have proven that the configuration of alpha-Me-benzyl connected with amide at C6 is essential for the binding affinity. The S-configured inhibitor (11j) displays 80 times more potency than the R-configure...

journal_title：Journal of computer-aided molecular design

authors： Chen Q,Cui W,Ji M

更新日期：2009-10-01 00:00:00

abstract：:Data driven decision making is a key element of today's pharmaceutical research, including early drug discovery. It comprises questions like which target to pursue, which chemical series to pursue, which compound to make next, or which compound to select for advanced profiling and promotion to pre-clinical development...

journal_title：Journal of computer-aided molecular design

authors： Beck B,Seeliger D,Kriegl JM

更新日期：2015-09-01 00:00:00

abstract：:As part of the fourth statistical assessment of modeling of proteins and ligands (sampl.eyesopen.com) prediction challenge, the strength of association of nine guests (1-9) binding to octa-acid host was determined by a combination of (1)H NMR and isothermal titration calorimetry. Association constants in sodium tetrab...

journal_title：Journal of computer-aided molecular design

authors： Gibb CL,Gibb BC

更新日期：2014-04-01 00:00:00

abstract：:Steric complementarity is a prerequisite for ligand-receptor recognition; this implies that drugs with a common receptor binding site should possess sterically similar binding surfaces. This principle is used as the basis for an automatic and unbiased method that superposes molecules. One molecule is rotated and trans...

journal_title：Journal of computer-aided molecular design

authors： Perkins TD,Mills JE,Dean PM

更新日期：1995-12-01 00:00:00

abstract：:We used blind predictions of the 47 hydration free energies in the SAMPL4 challenge to test multiple partial charge models in the context of explicit solvent free energy simulations with the general AMBER force field. One of the partial charge models, IPolQ-Mod, is a fast continuum solvent-based implementation of the ...

journal_title：Journal of computer-aided molecular design

authors： Muddana HS,Sapra NV,Fenley AT,Gilson MK

更新日期：2014-03-01 00:00:00

abstract：:The support vector machine, which is a novel algorithm from the machine learning community, was used to develop quantitation and classification models which can be used as a potential screening mechanism for a novel series of COX-2 selective inhibitors. Each compound was represented by calculated structural descriptor...

journal_title：Journal of computer-aided molecular design

authors： Liu HX,Zhang RS,Yao XJ,Liu MC,Hu ZD,Fan BT

更新日期：2004-06-01 00:00:00

abstract：:The project on crystallographic modelling aims at extending the application of interactive graphics to inorganic structures. Starting from the available expertise in organic and protein modelling, the symmetry of the crystal structure is used not only to draw fixed models of many unit cells of the structure, which as ...

journal_title：Journal of computer-aided molecular design

authors： Driessen RA,Loopstra BO,de Bruijn DP,Kuipers HP,Schenk H

更新日期：1988-10-01 00:00:00

abstract：:We have derived a model of the nicotinic acetylcholine binding site. This was accomplished by using three known agonists (acetylcholine, nicotine and epibatidine) as templates around which polypeptide side chains, found to be part of the receptor cavity from published molecular biology studies, are allowed to flow fre...

journal_title：Journal of computer-aided molecular design

authors： Gálvez-Ruano E,Iriepa-Canalda I,Morreale A,Lipkowitz KB

更新日期：1999-01-01 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

abstract：:Understanding how proteins encode ligand specificity is fascinating and similar in importance to deciphering the genetic code. For protein-ligand recognition, the combination of an almost infinite variety of interfacial shapes and patterns of chemical groups makes the problem especially challenging. Here we analyze da...

journal_title：Journal of computer-aided molecular design

authors： Raschka S,Wolf AJ,Bemister-Buffington J,Kuhn LA

更新日期：2018-04-01 00:00:00

abstract：:Atomic-resolution structures of the transmembrane 7-alpha-helical domains of 26 G-protein-coupled receptors (GPCRs) (including opsins, cationic amine, melatonin, purine, chemokine, opioid, and glycoprotein hormone receptors and two related proteins, retinochrome and Duffy erythrocyte antigen) were calculated by distan...

journal_title：Journal of computer-aided molecular design

authors： Lomize AL,Pogozheva ID,Mosberg HI

更新日期：1999-07-01 00:00:00

abstract：:A structure-binding activity relationship for the intestinal bile acid transporter has been developed using data from a series of bile acid analogs in a comparative molecular field analysis (CoMFA). The studied compounds consisted of a series of bile acid-peptide conjugates, with modifications at the 24 position of th...

journal_title：Journal of computer-aided molecular design

authors： Swaan PW,Szoka FC Jr,Oie S

更新日期：1997-11-01 00:00:00