Comparative molecular field analysis and energy interaction studies of thrombin-inhibitor complexes.

abstract：:Leishmania donovani dipeptidylcarboxypeptidsae (LdDCP), an angiotensin converting enzyme (ACE) related metallopeptidase has been identified and characterized as a putative drug target for antileishmanial chemotherapy. The kinetic parameters for LdDCP with substrate, Hip-His-Leu were determined as, Km, 4 mM and Vmax, 1...

journal_title：Journal of computer-aided molecular design

authors： Baig MS,Kumar A,Siddiqi MI,Goyal N

更新日期：2010-01-01 00:00:00

abstract：:Cheminformatics protocols have been developed and assessed that identify a small set of fragments which can represent the compounds in a chemical library for use in fragment-based ligand discovery. Six different methods have been implemented and tested on Input Libraries of compounds from three suppliers. The resultin...

journal_title：Journal of computer-aided molecular design

authors： Schulz MN,Landström J,Bright K,Hubbard RE

更新日期：2011-07-01 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：: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 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：:A series of non-peptide angiotensin II receptor antagonists was investigated with the aim of developing a 3D QSAR model using comparative molecular field analysis descriptors and approaches. The main goals of the study were dictated by an interest in methodologies and an understanding of the binding requirements to th...

journal_title：Journal of computer-aided molecular design

authors： Belvisi L,Bravi G,Catalano G,Mabilia M,Salimbeni A,Scolastico C

更新日期：1996-12-01 00:00:00

abstract：:The free fatty acid receptor 1 (FFAR1, formerly GPR40), is a potential G protein-coupled receptor (GPCR) target for the treatment of type 2 diabetes mellitus (T2DM), as it enhances glucose-dependent insulin secretion upon activation by endogenous long-chain free fatty acids. The presence of two allosterically communic...

journal_title：Journal of computer-aided molecular design

authors： Atanasio S,Deganutti G,Reynolds CA

更新日期：2020-11-01 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：: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：:Two different types of approaches: (a) approaches that combine quantitative structure activity relationships, quantum mechanical electronic structure methods, and machine-learning and, (b) electronic structure vertical solvation approaches, were used to predict the logP coefficients of 11 molecules as part of the SAMP...

journal_title：Journal of computer-aided molecular design

authors： Patel P,Kuntz DM,Jones MR,Brooks BR,Wilson AK

更新日期：2020-05-01 00:00:00

abstract：:Here, we report our results from quantitative structure-activity relationship studies on tyrosinase inhibitors. Interactions between benzoic acid derivatives and tyrosinase active sites were also studied using a molecular docking method. These studies indicated that one possible mechanism for the interaction between b...

journal_title：Journal of computer-aided molecular design

authors： Xue CB,Luo WC,Ding Q,Liu SZ,Gao XX

更新日期：2008-05-01 00:00:00

abstract：:Thirty-six compounds, representing six different structural classes of insecticides which are known to act at the gamma-aminobutyric acid receptor/chloride ionophore, have been superimposed by methods which maximise the commonality of steric and electrostatic fields. Maximal steric and electrostatic alignment was deri...

journal_title：Journal of computer-aided molecular design

authors： Calder JA,Wyatt JA,Frenkel DA,Casida JE

更新日期：1993-02-01 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：:Targeting Proviral integration-site of murine Moloney leukemia virus 1 kinase, hereafter called Pim-1 kinase, is a promising strategy for treating different kinds of human cancer. Headed for this a total list of 328 formerly reported Pim-1 kinase inhibitors has been explored and divided based on the pharmacophoric fea...

journal_title：Journal of computer-aided molecular design

authors： Shahin R,Swellmeen L,Shaheen O,Aboalhaija N,Habash M

更新日期：2016-01-01 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：:It is essential, in order to minimise expensive drug failures due to toxicity being found in late development or even in clinical trials, to determine potential toxicity problems as early as possible. In view of the large libraries of compounds now being handled by combinatorial chemistry and high-throughput screening...

journal_title：Journal of computer-aided molecular design

authors： Dearden JC

更新日期：2003-02-01 00:00:00

abstract：:An evolutionary algorithm was developed for fragment-based de novo design of molecules (TOPAS, TOPology-Assigning System). This stochastic method aims at generating a novel molecular structure mimicking a template structure. A set of approximately 25,000 fragment structures serves as the building block supply, which w...

journal_title：Journal of computer-aided molecular design

authors： Schneider G,Lee ML,Stahl M,Schneider P

更新日期：2000-07-01 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 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 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：: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：: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：:We present blind predictions submitted to the SAMPL5 challenge on calculating distribution coefficients. The predictions were based on estimating the solvation free energies in water and cyclohexane of the 53 compounds in the challenge. These free energies were computed using alchemical free energy simulations based o...

journal_title：Journal of computer-aided molecular design

authors： Genheden S,Essex JW

更新日期：2016-11-01 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：: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

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

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：:For computational de novo design, a general retrospective validation work is a very challenging task. Here we propose a comprehensive workflow to de novo design driven by the needs of computational and medicinal chemists and, at the same time, we propose a general validation scheme for this technique. The study was co...

journal_title：Journal of computer-aided molecular design

authors： Zaliani A,Boda K,Seidel T,Herwig A,Schwab CH,Gasteiger J,Claussen H,Lemmen C,Degen J,Pärn J,Rarey M

更新日期：2009-08-01 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：: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