A promising enantioselective Diels-Alder dienophile by computer-assisted rational design: 2,5-diphenyl-1-vinyl-borolane.

abstract：:A MD simulation protocol was developed to model halogen bonding in protein-ligand complexes by inclusion of a charged extra point to represent the anisotropic distribution of charge on the halogen atom. This protocol was then used to simulate the interactions of cathepsin L with a series of halogenated and non-halogen...

journal_title：Journal of computer-aided molecular design

authors： Celis-Barros C,Saavedra-Rivas L,Salgado JC,Cassels BK,Zapata-Torres G

更新日期：2015-01-01 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 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：:Electrostatic potential complementarity between ligands and their receptor sites is evaluated by the superposition of the electrostatic potential, generated by the receptor, onto the ligand potential over the ligand van der Waals surface. We would like to examine which structural factors generate this pattern of super...

journal_title：Journal of computer-aided molecular design

authors： Chau PL,Dean PM

更新日期：1994-10-01 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：: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：:In contrast to the computational generation of conventional tautomers, the analogous operation that would produce ring-chain tautomers is rarely available in cheminformatics codes. This is partly due to the perceived unimportance of ring-chain tautomerism and partly because specialized algorithms are required to reali...

journal_title：Journal of computer-aided molecular design

authors： Levine DS,Watson MA,Jacobson LD,Dickerson CE,Yu HS,Bochevarov AD

更新日期：2020-08-24 00:00:00

abstract：:The establishment of quantitative structure-activity relationship (QSAR) models for the toxicity of polycylic aromatic hydrocarbons (PAHs) is described. Two properties, in vitro percutaneous absorption in rat skin and discrete levels of carcinogenic activity, are examined using molecular quantum similarity measures (M...

journal_title：Journal of computer-aided molecular design

authors： Gallegos A,Robert D,Gironés X,Carbó-Dorca R

更新日期：2001-01-01 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：:A Comparative Molecular Field Analysis (CoMFA) and an interaction energy-based method were applied on a database holding the 3D structures of 29 thrombin-inhibitor complexes. Several parameters were optimized in both methods in order to obtain the best correlation between theoretical and experimentally determined bind...

journal_title：Journal of computer-aided molecular design

authors： Bursi R,Grootenhuis PD

更新日期：1999-05-01 00:00:00

abstract：:A method has been developed that allows one to drive a molecule to conformations of lowest energy given the starting conformation, the identity of the rotatable bonds and the step size. This method has proved useful in our hands in the drug design arena where it is frequently more important to get 'low-energy' conform...

journal_title：Journal of computer-aided molecular design

authors： Jaeger EP,Peterson ML,Treasurywala AM

更新日期：1995-02-01 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：:Pamidronate, alendronate, APHBP and neridronate are a group of drugs, known as second-generation bisphosphonates (2G-BPs), commonly used in the treatment of bone-resorption disorders, and recently their use has been related to some collateral side effects. The therapeutic activity of 2G-BPs is related to the inhibitio...

journal_title：Journal of computer-aided molecular design

authors： Fernández D,Ramis R,Ortega-Castro J,Casasnovas R,Vilanova B,Frau J

更新日期：2017-07-01 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：:Quantitative Structure-Activity Relationship (QSAR) models are critical in various areas of drug discovery, for example in lead optimisation and virtual screening. Recently, the need for models that are not only predictive but also interpretable has been highlighted. In this paper, a new methodology is proposed to bui...

journal_title：Journal of computer-aided molecular design

authors： Cardoso-Silva J,Papageorgiou LG,Tsoka S

更新日期：2019-09-01 00:00:00

abstract：:In the recent SAMPL5 challenge, participants submitted predictions for cyclohexane/water distribution coefficients for a set of 53 small molecules. Distribution coefficients (log D) replace the hydration free energies that were a central part of the past five SAMPL challenges. A wide variety of computational methods w...

journal_title：Journal of computer-aided molecular design

authors： Bannan CC,Burley KH,Chiu M,Shirts MR,Gilson MK,Mobley DL

更新日期：2016-11-01 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

abstract：:To generate reduced point charge models of proteins, we developed an original approach to hierarchically locate extrema in charge density distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential (MEP) functions. A charge fitting program was used to assign charge valu...

journal_title：Journal of computer-aided molecular design

authors： Leherte L,Vercauteren DP

更新日期：2011-10-01 00:00:00

abstract：:The linear finite difference Poisson-Boltzmann (FDPB) equation is applied to the calculation of the electrostatic binding free energies of a group of inhibitors to the Neuraminidase enzyme. An ensemble of enzyme-inhibitor complex conformations was generated using Monte Carlo simulations and the electrostatic binding f...

journal_title：Journal of computer-aided molecular design

authors： Woods CJ,King MA,Essex JW

更新日期：2001-02-01 00:00:00

abstract：:In the present work we have modeled the Michaelis complex of the cyclic-Adenosine Monophosphate Dependent (cAMD) Protein Kinase A (PKA) with Mg(2)ATP and the heptapeptide substrate Kemptide by classical molecular dynamics. The chosen synthetic substrate is relevant for its high efficiency and small size, and it has no...

journal_title：Journal of computer-aided molecular design

authors： Montenegro M,Garcia-Viloca M,González-Lafont A,Lluch JM

更新日期：2007-10-01 00:00:00

abstract：:Estimation of bioavailability and toxicity at the very beginning of the drug development process is one of the big challenges in drug discovery. Most of the processes involved in ADME are driven by rather unspecific interactions between drugs and biological macromolecules. Within the past decade, drug transport pumps ...

journal_title：Journal of computer-aided molecular design

authors： Klein C,Kaiser D,Kopp S,Chiba P,Ecker GF

更新日期：2002-11-01 00:00:00

abstract：:In this paper a database of small frequently occurring molecular fragments is used for the determination of fragment bond lengths from the Cambridge Structural Database. A large number of bond types are described that have not been reported previously. ...

journal_title：Journal of computer-aided molecular design

authors： Chau PL,Dean PM

更新日期：1992-08-01 00:00:00

abstract：:Manifold representations of rotational/translational motion and conformational space of a ligand were previously shown to be effective for local energy optimization. In this paper we report the development of the Monte-Carlo energy minimization approach (MCM), which uses the same manifold representation. The approach ...

journal_title：Journal of computer-aided molecular design

authors： Ignatov M,Liu C,Alekseenko A,Sun Z,Padhorny D,Kotelnikov S,Kazennov A,Grebenkin I,Kholodov Y,Kolosvari I,Perez A,Dill K,Kozakov D

更新日期：2019-01-01 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：: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：: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：: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：:This paper describes several case studies concerning protein function inference from its structure using our novel approach described in the accompanying paper. This approach employs family-specific motifs, i.e. three-dimensional amino acid packing patterns that are statistically prevalent within a protein family. For...

journal_title：Journal of computer-aided molecular design

authors： Bandyopadhyay D,Huan J,Prins J,Snoeyink J,Wang W,Tropsha A

更新日期：2009-11-01 00:00:00

abstract：:The Ligand Design (LUDI) approach has been used in order to design leucine aminopeptidase inhibitors, predict their activity and analyze their interactions with the enzyme. The investigation was based on the crystal structure of bovine lens leucine aminopeptidase (LAP) complexed with its inhibitor--the phosphonic acid...

journal_title：Journal of computer-aided molecular design

authors： Grembecka J,Sokalski WA,Kafarski P

更新日期：2000-08-01 00:00:00

abstract：:Accurate and well-curated experimental pKa data of organic acids and bases in both aqueous and non-aqueous media are invaluable in many areas of chemical research, including pharmaceutical, agrochemical, specialty chemical and property prediction research. In pharmaceutical research, pKa data are relevant in ligand de...

journal_title：Journal of computer-aided molecular design

authors： Slater AM

更新日期：2014-10-01 00:00:00