Prediction of the three-dimensional structure of the human Fas receptor by comparative molecular modeling.

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：:SIRT1 is an NAD+-dependent deacetylase, whose activators have potential therapeutic applications in the age-related, metabolic, neurode-generative and cardiovascular diseases. Resveratrol (RSV) has been regarded as potent SIRT1 activator in the treatment of atherosclerosis and cardiovascular diseases. Moreover, the pr...

journal_title：Journal of computer-aided molecular design

authors： Chen H,Wang Y,Gao Z,Yang W,Gao J

更新日期：2019-04-01 00:00:00

abstract：:Chemical space networks (CSNs) have recently been introduced as an alternative to other coordinate-free and coordinate-based chemical space representations. In CSNs, nodes represent compounds and edges pairwise similarity relationships. In addition, nodes are annotated with compound property information such as biolog...

journal_title：Journal of computer-aided molecular design

authors： Zhang B,Vogt M,Maggiora GM,Bajorath J

更新日期：2015-10-01 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：:De novo ligand design supports the search for novel molecular scaffolds in medicinal chemistry projects. This search can either be based on structural information of the targeted active site (structure-based approach) or on similarity to known binders (ligand-based approach). In the absence of structural information o...

journal_title：Journal of computer-aided molecular design

authors： Lippert T,Schulz-Gasch T,Roche O,Guba W,Rarey M

更新日期：2011-10-01 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：:Clarithromycin (6-O-methylerythromycin A) is a 14-membered macrolide antibiotic which is active in vitro against clinically important gram-positive and gram-negative bacteria. The selectivity of the methylation of the C-6 OH group is studied on erythromycin A derivatives. To understand the effect of the solvent on the...

journal_title：Journal of computer-aided molecular design

authors： Duran D,Aviyente V,Baysa C

更新日期：2004-02-01 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 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：: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：: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：:Lipophilicity, often expressed as distribution coefficients (log D) in octanol/water, is an important physicochemical parameter influencing processes such as oral absorption, brain uptake and various pharmacokinetic (PK) properties. Increasing log D values increases oral absorption, plasma protein binding and volume o...

journal_title：Journal of computer-aided molecular design

authors： van de Waterbeemd H,Smith DA,Jones BC

更新日期：2001-03-01 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：: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：: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：: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：: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：: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：: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：: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：: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：: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：: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：: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：:We have used the Chemical Structure DataBase (CSDB) of the NCI CADD Group, an aggregated collection of over 150 small-molecule databases totaling 103.5 million structure records, to conduct tautomerism analyses on one of the largest currently existing sets of real (i.e. not computer-generated) compounds. This analysis...

journal_title：Journal of computer-aided molecular design

authors： Sitzmann M,Ihlenfeldt WD,Nicklaus MC

更新日期：2010-06-01 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：:Molecular dynamics simulations of complexes between Norwalk virus RNA dependent RNA polymerase and its natural CTP and 2dCTP (both containing the O5'-C5'-C4'-O4' sequence of atoms bridging the triphosphate and sugar moiety) or modified coCTP (C5'-O5'-C4'-O4'), cocCTP (C5'-O5'-C4'-C4'') substrates were produced by mean...

journal_title：Journal of computer-aided molecular design

authors： Maláč K,Barvík I

更新日期：2013-04-01 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：:We describe the performance of multiple pose prediction methods for the D3R 2016 Grand Challenge. The pose prediction challenge includes 36 ligands, which represent 4 chemotypes and some miscellaneous structures against the FXR ligand binding domain. In this study we use a mix of fully automated methods as well as hum...

journal_title：Journal of computer-aided molecular design

authors： Fradera X,Verras A,Hu Y,Wang D,Wang H,Fells JI,Armacost KA,Crespo A,Sherborne B,Wang H,Peng Z,Gao YD

更新日期：2018-01-01 00:00:00