New designs for MRI contrast agents.

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：: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：: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：: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：:Computational protein binding affinity prediction can play an important role in drug research but performing efficient and accurate binding free energy calculations is still challenging. In the context of phase 2 of the Drug Design Data Resource (D3R) Grand Challenge 2 we used our automated eTOX ALLIES approach to app...

journal_title：Journal of computer-aided molecular design

authors： Rifai EA,van Dijk M,Vermeulen NPE,Geerke DP

更新日期：2018-01-01 00:00:00

abstract：:Combining Lipinski's rule with the docking and steered molecular dynamics simulations and using the PubChem data base of about 1.4 million compounds, we have obtained DNA dyes Hoechst 34580 and Hoechst 33342 as top-leads for the Alzheimer's disease. The binding properties of these ligands to amyloid beta (Aβ) fibril w...

journal_title：Journal of computer-aided molecular design

authors： Thai NQ,Tseng NH,Vu MT,Nguyen TT,Linh HQ,Hu CK,Chen YR,Li MS

更新日期：2016-08-01 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 overexpression and/or mutation of the epidermal growth factor receptor (EGFR) tyrosine kinase has been observed in many human solid tumors, and is under intense investigation as a novel anticancer molecular target. Comparative 3D-QSAR analyses using different alignments were undertaken employing comparative molecu...

journal_title：Journal of computer-aided molecular design

authors： Assefa H,Kamath S,Buolamwini JK

更新日期：2003-08-01 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 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 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：: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：:While it may seem intuitive that using an ensemble of multiple conformations of a receptor in structure-based virtual screening experiments would necessarily yield improved enrichment of actives relative to using just a single receptor, it turns out that at least in the p38 MAP kinase model system studied here, a very...

journal_title：Journal of computer-aided molecular design

authors： Rao S,Sanschagrin PC,Greenwood JR,Repasky MP,Sherman W,Farid R

更新日期：2008-09-01 00:00:00

abstract：:We present three complementary approaches for score-tuning that improve docking performance in pose prediction, virtual screening and binding affinity assessment. The methodology utilizes experimental data to customize the scoring function for the system of interest considering the specific docking scenario. The tunin...

journal_title：Journal of computer-aided molecular design

authors： Ravitz O,Zsoldos Z,Simon A

更新日期：2011-11-01 00:00:00

abstract：:The mounting evidences have shown that signal transducer and activator of transcription 3 (Stat3) is a critical target for cancer therapy. Recently, we developed a G-quartet oligonucleotide T40214 as a novel and potent Stat3 inhibitor. T40214 specifically inhibited DNA-binding activity of Stat3 and significantly suppr...

journal_title：Journal of computer-aided molecular design

authors： Zhu Q,Jing N

更新日期：2007-10-01 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：: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：: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：:Structure-based drug design (SBDD) has matured within the last two decades as a valuable tool for the optimization of low molecular weight lead compounds to highly potent drugs. The key step in SBDD requires knowledge of the three-dimensional structure of the target-ligand complex, which is usually determined by X-ray...

journal_title：Journal of computer-aided molecular design

authors： Salmaso V,Sturlese M,Cuzzolin A,Moro S

更新日期：2016-09-01 00:00:00

abstract：:Molecular modeling techniques and three-dimensional (3D) pattern analysis have been used to investigate the chemical and steric properties of compounds that inhibit transport of the plant hormone auxin. These compounds bind to a specific site on the plant plasma membrane characterized by its affinity for the herbicide...

journal_title：Journal of computer-aided molecular design

authors： Bures MG,Black-Schaefer C,Gardner G

更新日期：1991-08-01 00:00:00

abstract：:We have undertaken molecular dynamics simulations on the d(CGCAAAAAAGCG).d(CGCTTTTTTGCG) dodecamer in solution. In this study, we focus on aspects of conformation and dynamics, including the possibility of cross-strand hydrogen bonds. We compare our results with those from crystallography as well as infrared, Raman an...

journal_title：Journal of computer-aided molecular design

authors： de Souza ON,Goodfellow JM

更新日期：1994-06-01 00:00:00

abstract：:The Multiple Copy Simultaneous Search methodology has been used to construct functionality maps for an extended region of human thrombin, including the active site. This method allows the determination of energetically favorable positions and orientations for functional groups defined by the user on the three-dimensio...

journal_title：Journal of computer-aided molecular design

authors： Grootenhuis PD,Karplus M

更新日期：1996-02-01 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：: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：: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 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：: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：: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：:The "embedded cluster reference interaction site model" (EC-RISM) integral equation theory is applied to the problem of predicting aqueous pKa values for drug-like molecules based on an ensemble of tautomers. EC-RISM is based on self-consistent calculations of a solute's electronic structure and the distribution funct...

journal_title：Journal of computer-aided molecular design

authors： Tielker N,Eberlein L,Güssregen S,Kast SM

更新日期：2018-10-01 00:00:00