Coupling constants again: experimental restraints in structure refinement.

abstract：:Histo-blood group ABH antigens serve as recognition sites for infectious microorganisms and tissue lectins in intercellular communication, e.g. in tumor progression. Thus, they are of interest as a starting point for drug design. In this respect, potent non-hydrolysable derivatives such as thioglycosides are of specia...

journal_title：Journal of computer-aided molecular design

authors： Strino F,Lii JH,Gabius HJ,Nyholm PG

更新日期：2009-12-01 00:00:00

abstract：:The aspartate protease of the human immune deficiency type-1 virus (HIV-1) has become a crucial antiviral target in which many useful antiretroviral inhibitors have been developed. However, it seems the emergence of new HIV-1 PR mutations enhances drug resistance, hence, the available FDA approved drugs show less acti...

journal_title：Journal of computer-aided molecular design

authors： Sanusi ZK,Govender T,Maguire GEM,Maseko SB,Lin J,Kruger HG,Honarparvar B

更新日期：2018-03-01 00:00:00

abstract：:Using the X-ray crystal structure of the human topoisomerase I (top1) - DNA cleavable complex and the Sybyl software package, we have developed a general model for the ternary cleavable complex formed with four protoberberine alkaloids differing in the substitution on the terminal phenyl rings and covering a broad ran...

journal_title：Journal of computer-aided molecular design

authors： Kettmann V,Kost'álová D,Höltje HD

更新日期：2004-12-01 00:00:00

abstract：:We employed a combination of molecular docking and dynamics to understand the interaction of three different radical scavengers (SB-HSC21, ABNM13 and trimidox) with ribonucleotide reductase M2 (hRRM2) domain. On the basis of the observed results, we can propose how these ligands interact with the enzyme, and cease the...

journal_title：Journal of computer-aided molecular design

authors： Basu A,Sinha BN

更新日期：2012-07-01 00:00:00

abstract：:A new computer program is described, which positions small molecules into clefts of protein structures (e.g. an active site of an enzyme) in such a way that hydrogen bonds can be formed with the enzyme and hydrophobic pockets are filled with hydrophobic groups. The program works in three steps. First it calculates int...

journal_title：Journal of computer-aided molecular design

authors： Böhm HJ

更新日期：1992-02-01 00:00:00

abstract：:All-atom molecular dynamics computer simulations were used to blindly predict the hydration free energies of a range of chloro-organic compounds as part of the SAMPL3 challenge. All compounds were parameterized within the framework of the OPLS-AA force field, using an established protocol to compute the absolute hydra...

journal_title：Journal of computer-aided molecular design

authors： Beckstein O,Iorga BI

更新日期：2012-05-01 00:00:00

abstract：:A new and rigorous method for the fractional description of solvation and transfer free energies is presented. The method is based on the use of the Miertus-Scrocco-Tomasi self-consistent reaction field method (MST-SCRF), and allows for a rigorous partition of the total solvation free energy into surface elements. The...

journal_title：Journal of computer-aided molecular design

authors： Luque FJ,Barril X,Orozco M

更新日期：1999-03-01 00:00:00

abstract：:Quantitative Structure-Activity Relationship (QSAR) models are used increasingly to screen chemical databases and/or virtual chemical libraries for potentially bioactive molecules. These developments emphasize the importance of rigorous model validation to ensure that the models have acceptable predictive power. Using...

journal_title：Journal of computer-aided molecular design

authors： Golbraikh A,Shen M,Xiao Z,Xiao YD,Lee KH,Tropsha A

更新日期：2003-02-01 00:00:00

abstract：:A dataset of 82 protein-ligand complexes of known 3D structure and binding constant Ki was analysed to elucidate the important factors that determine the strength of protein-ligand interactions. The following parameters were investigated: the number and geometry of hydrogen bonds and ionic interactions between the pro...

journal_title：Journal of computer-aided molecular design

authors： Böhm HJ

更新日期：1998-07-01 00:00:00

abstract：:An empirical hydrophobic field-like 3D function has been calculated with the program HINT (hydrophobic interactions) and imported into the SYBYL implementation of CoMFA (Comparative Molecular Field Analysis). The addition of hydrophobicity appears to offer increased chemical interpretability of CoMFA models. An exampl...

journal_title：Journal of computer-aided molecular design

authors： Kellogg GE,Semus SF,Abraham DJ

更新日期：1991-12-01 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：: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：: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：: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：:ERG-associated protein with the SET domain (ESET/SET domain bifurcated 1/SETDB1/KMT1E) is a histone lysine methyltransferase (HKMT) and it preferentially tri-methylates lysine 9 of histone H3 (H3K9me3). SETDB1/ESET leads to heterochromatin condensation and epigenetic gene silencing. These functional changes are report...

journal_title：Journal of computer-aided molecular design

authors： Park I,Hwang YJ,Kim T,Viswanath ANI,Londhe AM,Jung SY,Sim KM,Min SJ,Lee JE,Seong J,Kim YK,No KT,Ryu H,Pae AN

更新日期：2017-10-01 00:00:00

abstract：:We introduce the QuanSA method for inducing physically meaningful field-based models of ligand binding pockets based on structure-activity data alone. The method is closely related to the QMOD approach, substituting a learned scoring field for a pocket constructed of molecular fragments. The problem of mutual ligand a...

journal_title：Journal of computer-aided molecular design

authors： Cleves AE,Jain AN

更新日期：2018-07-01 00:00:00

abstract：:The use of MP2 level quantum mechanical (QM) calculations on isolated heteroaromatic ring systems for the prediction of the tautomeric propensities of whole molecules in a crystalline environment was examined. A Polarisable Continuum Model was used in the calculations to account for environment effects on the tautomer...

journal_title：Journal of computer-aided molecular design

authors： Cruz-Cabeza AJ,Schreyer A,Pitt WR

更新日期：2010-06-01 00:00:00

abstract：:Poly(amidoamine) (PAMAM) dendrimers have been extensively studied as delivery vectors in biomedical applications. A limited number of molecular dynamics (MD) simulation studies have investigated the effect of surface chemistry on therapeutic molecules loading, with the aim of providing insights for biocompatibility im...

journal_title：Journal of computer-aided molecular design

authors： Badalkhani-Khamseh F,Ebrahim-Habibi A,Hadipour NL

更新日期：2017-12-01 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：: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：: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：:Inducible, microsomal prostaglandin E synthase 1 (mPGES-1), the terminal enzyme in the prostaglandin (PG) biosynthetic pathway, constitutes a promising therapeutic target for the development of new anti-inflammatory drugs. To elucidate structure-function relationships and to enable structure-based design, an mPGES-1 h...

journal_title：Journal of computer-aided molecular design

authors： Xing L,Kurumbail RG,Frazier RB,Davies MS,Fujiwara H,Weinberg RA,Gierse JK,Caspers N,Carter JS,McDonald JJ,Moore WM,Vazquez ML

更新日期：2009-01-01 00:00:00

abstract：:We have developed PLASS (Protein-Ligand Affinity Statistical Score), a pair-wise potential of mean-force for rapid estimation of the binding affinity of a ligand molecule to a protein active site. This scoring function is derived from the frequency of occurrence of atom-type pairs in crystallographic complexes taken f...

journal_title：Journal of computer-aided molecular design

authors： Ozrin VD,Subbotin MV,Nikitin SM

更新日期：2004-04-01 00:00:00

abstract：:The design of molecules with desired properties is still a challenge because of the largely unpredictable end results. Computational methods can be used to assist and speed up this process. In particular, genetic algorithms have proved to be powerful tools with a wide range of applications, e.g. in the field of drug d...

journal_title：Journal of computer-aided molecular design

authors： Kamphausen S,Höltge N,Wirsching F,Morys-Wortmann C,Riester D,Goetz R,Thürk M,Schwienhorst A

更新日期：2002-08-01 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：: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 CASE (Computer Automated Structure Evaluation) program, with the aid of a geometry index for discriminating cis and trans isomers, has been used to study a set of retinoids tested for teratogenicity in hamsters. CASE identified 8 fragments, the most important representing the non-polar terminus of a retinoid with ...

journal_title：Journal of computer-aided molecular design

authors： Klopman G,Dimayuga ML

更新日期：1990-06-01 00:00:00

abstract：:The de novo design program Skelgen has been used to design inhibitor structures for four targets of pharmaceutical interest. The designed structures are compared to modeled binding modes of known inhibitors (i) visually and (ii) by means of a novel similarity measure considering the size and spatial proximity of the m...

journal_title：Journal of computer-aided molecular design

authors： Stahl M,Todorov NP,James T,Mauser H,Boehm HJ,Dean PM

更新日期：2002-07-01 00:00:00

abstract：:Pharmacophore methods provide a way of establishing a structure activity relationship for a series of known active ligands. Often, there are several plausible hypotheses that could explain the same set of ligands and, in such cases, it is important that the chemist is presented with alternatives that can be tested wit...

journal_title：Journal of computer-aided molecular design

authors： Cottrell SJ,Gillet VJ,Taylor R,Wilton DJ

更新日期：2004-11-01 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