Journal of Computer-Aided Molecular Design
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Application of multivariate data analysis methods to Comparative Molecular Field Analysis (CoMFA) data: Proton affinities and pKa prediction for nucleic acids components
Journal of Computer-Aided Molecular Design - Tập 13 - Trang 611-623 - 1999
Multivariate data analysis methods (Principal Component Analysis (PCA) and Partial Least Squares (PLS)) are applied to the analysis of the CoMFA (Comparative Molecular Field Analysis) data for several nucleic acids components. The data set includes nitrogenated bases, nucleosides, linear nucleotides, 3′, 5′-cyclic nucleotides and oligonucleotides. PCA is applied to study the structure of the CoMFA...... hiện toàn bộ
First virtual screening and experimental validation of inhibitors targeting GES-5 carbapenemase
Journal of Computer-Aided Molecular Design - Tập 33 Số 2 - Trang 295-305 - 2019
The SAMPL5 host–guest challenge: computing binding free energies and enthalpies from explicit solvent simulations by the attach-pull-release (APR) method
Journal of Computer-Aided Molecular Design - Tập 31 - Trang 133-145 - 2016
The absolute binding free energies and binding enthalpies of twelve host–guest systems in the SAMPL5 blind challenge were computed using our attach-pull-release (APR) approach. This method has previously shown good correlations between experimental and calculated binding data in retrospective studies of cucurbit[7]uril (CB7) and β-cyclodextrin (βCD) systems. In the present work, the computed bindi...... hiện toàn bộ
DFT calculation of four new potential agents muscarinic of bispyridinium type: structure, synthesis, biological activity, hydration, and relations with the potents W84 and DUO-3O
Journal of Computer-Aided Molecular Design - Tập 25 - Trang 145-161 - 2010
Four new potential agents muscarinic (allosteric modulators) were synthesized and studied by using the B3LYP density functional method. The optimum conformation and geometry structure of these compounds were determined and analyzed. Solvent effects were considered including a variable number (1–15) of explicit water molecules surrounding the compound in order to simulate the first hydration shell,...... hiện toàn bộ
A Monte Carlo pharmacophore generation procedure: Application to the human PAF receptor
Journal of Computer-Aided Molecular Design - Tập 7 - Trang 515-534 - 1993
A novel pharmacophore definition procedure is described, which uses a Monte Carlo method to superimpose molecules. Pharmacophore space is searched by a technique similar to high temperature annealing. Subsequent refinement of candidate pharmacophores by energy minimization produces low-energy conformations that may be involved in receptor binding. The method has been applied to compounds that bind...... hiện toàn bộ
The sequence homologies of cytochromes P-450 and active-site geometries
Journal of Computer-Aided Molecular Design - Tập 6 Số 3 - Trang 235-252 - 1992
A genetic algorithm for the automated generation of small organic molecules: Drug design using an evolutionary algorithm
Journal of Computer-Aided Molecular Design - Tập 14 - Trang 449-466 - 2000
Rational drug design involves finding solutions to large combinatorial problems for which an exhaustive search is impractical. Genetic algorithms provide a novel tool for the investigation of such problems. These are a class of algorithms that mimic some of the major characteristics of Darwinian evolution. LEA has been designed in order to conceive novel small organic molecules which satisfy quant...... hiện toàn bộ
Structural insights into transient receptor potential vanilloid type 1 (TRPV1) from homology modeling, flexible docking, and mutational studies
Journal of Computer-Aided Molecular Design - Tập 25 - Trang 317-327 - 2011
The transient receptor potential vanilloid subtype 1 (TRPV1) is a non-selective cation channel composed of four monomers with six transmembrane helices (TM1–TM6). TRPV1 is found in the central and peripheral nervous system, and it is an important therapeutic target for pain relief. We describe here the construction of a tetrameric homology model of rat TRPV1 (rTRPV1). We experimentally evaluated b...... hiện toàn bộ
MS-WHIM, new 3D theoretical descriptors derived from molecular surface properties: A comparative 3D QSAR study in a series of steroids
Journal of Computer-Aided Molecular Design - Tập 11 - Trang 79-92 - 1997
The recently proposed WHIM (Weighted Holistic Invariant Molecular) approach [Todeschini,R., Lasagni, M. and Marengo, E., J. Chemometrics, 8 (1994) 263] has been applied tomolecular surfaces to derive new 3D theoretical descriptors, called MS-WHIM. To test theirreliability, a 3D QSAR study has been performed on a series of steroids, comparing the MS-WHIM description to both the original WHIM indice...... hiện toàn bộ
Dự đoán độ gắn kết của ligand bằng phương pháp năng lượng tương tác tuyến tính Dịch bởi AI
Journal of Computer-Aided Molecular Design - Tập 12 - Trang 27-35 - 1998
Một phương pháp gần đây để ước lượng độ gắn kết của ligand đã được mở rộng. Phương pháp này sử dụng trung bình các thành phần năng lượng tương tác từ mô phỏng động lực học phân tử hoặc các kỹ thuật lấy mẫu tuần hoàn nhiệt khác. Việc kết hợp các sai lệch hệ thống từ phản ứng tuyến tính tĩnh điện, được rút ra từ các nghiên cứu rối loạn năng lượng tự do, vào biểu thức năng lượng tự do tuyệt đối của đ...... hiện toàn bộ
#độ gắn kết ligand #năng lượng tương tác #mô phỏng động lực học phân tử #thiết kế thuốc
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