QSPR modeling of UV absorption intensities.

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 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：: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：:Macroscopic pKa values were calculated for all compounds in the SAMPL6 blind prediction challenge, based on quantum chemical calculations with a continuum solvation model and a linear correction derived from a small training set. Microscopic pKa values were derived from the gas-phase free energy difference between pro...

journal_title：Journal of computer-aided molecular design

authors： Selwa E,Kenney IM,Beckstein O,Iorga BI

更新日期：2018-10-01 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 Fas antigen, a cell surface receptor belonging to the tumor necrosis factor receptor (TNFR) superfamily, triggers programmed cell death (apoptosis) in the immune system. The three-dimensional structure of Fas and molecular details of the interaction between Fas and its ligand are currently unknown. A three-dimensi...

journal_title：Journal of computer-aided molecular design

authors： Bajorath J,Aruffo A

更新日期：1997-01-01 00:00:00

abstract：:The Epstein-Barr Nuclear Antigen 1 (EBNA1) is a critical protein encoded by the Epstein-Barr Virus (EBV). During latent infection, EBNA1 is essential for DNA replication and transcription initiation of viral and cellular genes and is necessary to immortalize primary B-lymphocytes. Nonetheless, the concept of EBNA1 as ...

journal_title：Journal of computer-aided molecular design

authors： Gianti E,Messick TE,Lieberman PM,Zauhar RJ

更新日期：2016-04-01 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 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：: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：:In this paper we describe our approaches to predict the binding mode of twenty BACE1 ligands as part of Grand Challenge 4 (GC4), organized by the Drug Design Data Resource. Calculations for all submissions (except for one, which used AutoDock4.2) were performed using AutoDock-GPU, the new GPU-accelerated version of Au...

journal_title：Journal of computer-aided molecular design

authors： Santos-Martins D,Eberhardt J,Bianco G,Solis-Vasquez L,Ambrosio FA,Koch A,Forli S

更新日期：2019-12-01 00:00:00

abstract：:The electron-conformational (EC) method in QSAR problems employs a unique (based on first principles) descriptor of molecular properties that incorporates the electronic structure and topology of the molecule and is presented in a digital-matrix form suitable for computer processing, the EC matrix of congruity (ECMC)....

journal_title：Journal of computer-aided molecular design

authors： Bersuker IB

更新日期：2008-06-01 00:00:00

abstract：:Dengue and related flaviviruses represent a significant global health threat. The envelope glycoprotein E mediates virus attachment to a host cell and the subsequent fusion of viral and host cell membranes. The fusion process is driven by conformational changes in the E protein and is an essential step in the virus li...

journal_title：Journal of computer-aided molecular design

authors： Yennamalli R,Subbarao N,Kampmann T,McGeary RP,Young PR,Kobe B

更新日期：2009-06-01 00:00:00

abstract：:R67 dihydrofolate reductase (DHFR), a bacterial plasmid-encoded enzyme associated with resistance to the drug trimethoprim, shows neither sequence nor structural homology with the chromosomal DHFR. It presents a highly symmetrical toroidal structure, where four identical monomers contribute to the unique central activ...

journal_title：Journal of computer-aided molecular design

authors： Alonso H,Gillies MB,Cummins PL,Bliznyuk AA,Gready JE

更新日期：2005-03-01 00:00:00

abstract：:AstexViewer is a Java molecular graphics program that can be used for visualisation in many aspects of structure-based drug design. This paper describes its functionality, implementation and examples of its use. The program can run as an Applet in a web browser allowing structures to be displayed without installing ad...

journal_title：Journal of computer-aided molecular design

authors： Hartshorn MJ

更新日期：2002-12-01 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：: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 process of compound selection and prioritization is crucial for both combinatorial chemistry (CBC) and high throughput screening (HTS). Compound libraries have to be screened for unwanted chemical structures, as well as for unwanted chemical properties. Property extrema can be eliminated by using property filters,...

journal_title：Journal of computer-aided molecular design

authors： Oprea TI

更新日期：2000-03-01 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：:We have developed quantitative structure-activity relationship (QSAR) models for 44 non-nucleoside HIV-1 reverse transcriptase inhibitors (NNRTIs) of the pyridinone derivative type. The k nearest neighbor (kNN) variable selection approach was used. This method utilizes multiple descriptors such as molecular connectivi...

journal_title：Journal of computer-aided molecular design

authors： Medina-Franco JL,Golbraikh A,Oloff S,Castillo R,Tropsha A

更新日期：2005-04-01 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：: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 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：: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：:We report the implementation of molecular modeling approaches developed as a part of the 2016 Grand Challenge 2, the blinded competition of computer aided drug design technologies held by the D3R Drug Design Data Resource ( https://drugdesigndata.org/ ). The challenge was focused on the ligands of the farnesoid X rece...

journal_title：Journal of computer-aided molecular design

authors： Yakovenko O,Jones SJM

更新日期：2018-01-01 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：: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：:Starting from the X-ray structure of a class I major histocompatibility complex (MHC)-encoded protein (HLA-B*2705), a naturally presented self-nonapeptide and two synthetic analogues were simulated in the binding groove of two human leukocyte antigen (HLA) alleles (B*2703 and B*2705) differing in a single amino acid r...

journal_title：Journal of computer-aided molecular design

authors： Rognan D,Krebs S,Kuonen O,Lamas JR,López de Castro JA,Folkers G

更新日期：1997-09-01 00:00:00

abstract：:Optimization in medicinal chemistry often involves designing replacements for a section of a molecule which aim to retain potency while improving other properties of the compound. In this study, we perform a retrospective analysis using a number of computational methods to identify active side chains amongst a pool of...

journal_title：Journal of computer-aided molecular design

authors： Baumgartner MP,Evans DA

更新日期：2020-09-01 00:00:00

abstract：:Fast Fourier transform (FFT) based approaches have been successful in application to modeling of relatively rigid protein-protein complexes. Recently, we have been able to adapt the FFT methodology to treatment of flexible protein-peptide interactions. Here, we report our latest attempt to expand the capabilities of t...

journal_title：Journal of computer-aided molecular design

authors： Padhorny D,Hall DR,Mirzaei H,Mamonov AB,Moghadasi M,Alekseenko A,Beglov D,Kozakov D

更新日期：2018-01-01 00:00:00