Comparison of commercially available genetic algorithms: gas as variable selection tool.

abstract：:Furanopyrimidine 1 (IC50 = 273 nM, LE = 0.36, LELP = 10.28) was recently identified by high-throughput screening (HTS) of an in-house library (125,000 compounds) as an Aurora kinase inhibitor. Structure-based hit optimization resulted in lead molecules with in vivo efficacy in a mouse tumour xenograft model, but no or...

journal_title：Journal of computer-aided molecular design

authors： Sarvagalla S,Singh VK,Ke YY,Shiao HY,Lin WH,Hsieh HP,Hsu JT,Coumar MS

更新日期：2015-01-01 00:00:00

abstract：:Aligning and overlaying two or more bio-active molecules is one of the key tasks in computational drug discovery and bio-activity prediction. Especially chemical-functional molecule characteristics from the view point of a macromolecular target represented as a 3D pharmacophore are the most interesting similarity meas...

journal_title：Journal of computer-aided molecular design

authors： Wolber G,Dornhofer AA,Langer T

更新日期：2006-12-01 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

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 conformational preferences of 12 molecular substructures in the crystalline state have been determined and compared with those predicted for relevant model compounds by ab initio molecular orbital calculations. Least-squares regression shows that there is a statistically significant correlation between the crystal...

journal_title：Journal of computer-aided molecular design

authors： Allen FH,Harris SE,Taylor R

更新日期：1996-06-01 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：:Quantitative structure-property relationship (QSPR) modeling of stability constants for the metal:ligand ratio 1:1 (logK) and 1:2 (logβ2) complexes of 3 transition metal ions with diverse organic ligands in aqueous solution was performed using ensemble multiple linear regression analysis and substructural molecular fr...

journal_title：Journal of computer-aided molecular design

authors： Solov'ev V,Varnek A,Tsivadze A

更新日期：2014-05-01 00:00:00

abstract：:The pharmacophoric concept plays an important role in ligand-based drug design methods to describe the similarity and diversity of molecules, and could also be exploited as a molecular representation scheme. A three-point pharmacophore method was used as a molecular representation perception. This procedure was implem...

journal_title：Journal of computer-aided molecular design

authors： Atlamazoglou V,Thireou T,Eliopoulos E

更新日期：2007-05-01 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：:Recently, we reported structurally novel PDE4 inhibitors based on 1,4-benzodiazepine derivatives. The main interest in developing bezodiazepine-based PDE4 inhibitors is in their lack of adverse effects of emesis with respect to rolipram-like compounds. A large effort has thus been made toward the structural optimizati...

journal_title：Journal of computer-aided molecular design

authors： Ducrot P,Andrianjara CR,Wrigglesworth R

更新日期：2001-09-01 00:00:00

abstract：:Formyl-peptide receptors (FPRs) belong to the family A of the G-protein coupled receptor superfamily and include three subtypes: FPR, FPR-like-1 and FPR-like-2. They have been involved in the control of many inflammatory processes promoting the recruitment and infiltration of leukocytes in regions of inflammation thro...

journal_title：Journal of computer-aided molecular design

authors： Ferrari C,Macchiarulo A,Costantino G,Pellicciari R

更新日期：2006-05-01 00:00:00

abstract：:The binding mode of (2S)-2-[4-[[(3S)-1-acetimidoyl-3-pyrrolidinyl]oxy]phenyl]-3-(7-ami dino-2- naphthyl)propanoic acid hydrochloride (DX-9065a, 4) to Factor Xa is examined using inhibition data for a series of analogs that have a hydrophobic group as well as basic or dibasic functionality. Comparative molecular field ...

journal_title：Journal of computer-aided molecular design

authors： Vaz RJ,McLean LR,Pelton JT

更新日期：1998-03-01 00:00:00

abstract：:A set of algorithms designed to enhance the display of protein binding cavities is presented. These algorithms, collectively entitled CAVITY SEARCH, allow the user to isolate and fully define the extent of a particular cavity. Solid modeling techniques are employed to produce a detailed cast of the active site region,...

journal_title：Journal of computer-aided molecular design

authors： Ho CM,Marshall GR

更新日期：1990-12-01 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：:Molecular modeling techniques and three-dimensional (3D) pattern analysis have been used to investigate the chemical and steric properties of compounds that inhibit transport of the plant hormone auxin. These compounds bind to a specific site on the plant plasma membrane characterized by its affinity for the herbicide...

journal_title：Journal of computer-aided molecular design

authors： Bures MG,Black-Schaefer C,Gardner G

更新日期：1991-08-01 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：:Benchmarks for molecular docking have historically focused on re-docking the cognate ligand of a well-determined protein-ligand complex to measure geometric pose prediction accuracy, and measurement of virtual screening performance has been focused on increasingly large and diverse sets of target protein structures, c...

journal_title：Journal of computer-aided molecular design

authors： Spitzer R,Jain AN

更新日期：2012-06-01 00:00:00

abstract：:In this work, we present a case study to explore the challenges associated with finding novel molecules for a receptor that has been studied in depth and has a wealth of chemical information available. Specifically, we apply a previously described protocol that incorporates explicit water molecules in the ligand bindi...

journal_title：Journal of computer-aided molecular design

authors： Lenselink EB,Beuming T,van Veen C,Massink A,Sherman W,van Vlijmen HW,IJzerman AP

更新日期：2016-10-01 00:00:00

abstract：:In a previous paper, we have shown the utility of cluster analysis for identifying patterns in the way the C alpha atoms of fragments of the beta-turn are distributed in three dimensions. This work has been extended to the C alpha-C beta bond vectors of 2- and 3-side-chain fragments. Again, distinct patterns emerge an...

journal_title：Journal of computer-aided molecular design

authors： Garland SL,Dean PM

更新日期：1999-09-01 00:00:00

abstract：:In virtual drug screening, the chemical diversity of hits is an important factor, along with their predicted activity. Moreover, interim results are of interest for directing the further research, and their diversity is also desirable. In this paper, we consider a problem of obtaining a diverse set of virtual screenin...

journal_title：Journal of computer-aided molecular design

authors： Nikitina N,Ivashko E,Tchernykh A

更新日期：2018-02-01 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：: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：: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：:Feature selection is commonly used as a preprocessing step to machine learning for improving learning performance, lowering computational complexity and facilitating model interpretation. This paper proposes the application of boosting feature selection to improve the classification performance of standard feature sel...

journal_title：Journal of computer-aided molecular design

authors： Cerruela García G,García-Pedrajas N

更新日期：2018-11-01 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 kinase-regulatory cell signaling networks play a central role in the pathogenesis of human cervical cancer (hCC). However, only few kinase inhibitors have been successfully developed for treatment of this cancer to date. Considering that the active sites of protein kinases are highly conserved and small-molecule i...

journal_title：Journal of computer-aided molecular design

authors： Han M,Sun D

更新日期：2019-07-01 00:00:00

abstract：:The similarity between Plasmodium falciparum phosphodiesterase enzymes (PfPDEs) and their human counterparts have been examined and human PDE9A was found to be a suitable template for the construction of homology models for each of the four PfPDE isoforms. In contrast, the architecture of the active sites of each mode...

journal_title：Journal of computer-aided molecular design

authors： Howard BL,Thompson PE,Manallack DT

更新日期：2011-08-01 00:00:00

abstract：:Both society and industry are interested in increasing the safety of pharmaceuticals. Potentially dangerous compounds could be filtered out at early stages of R&D by computer prediction of biological activity and ADMET characteristics. Accuracy of such predictions strongly depends on the quality & quantity of informat...

journal_title：Journal of computer-aided molecular design

authors： Filimonov D,Poroikov V

更新日期：2005-09-01 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：:In this work the rigid-analogue approach has been used to obtain information on the active conformation(s) of the calcium antagonist verapamil. A series of semi-rigid analogues of verapamil were synthesized and their biological activities evaluated on guinea-pig heart and aorta. These molecules were analysed by means ...

journal_title：Journal of computer-aided molecular design

authors： Romanelli MN,Dei S,Scapecchi S,Teodori E,Gualtieri F,Budriesi R,Mannhold R

更新日期：1994-04-01 00:00:00