Journal of Computer-Aided Molecular Design

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The need for scientific software engineering in the pharmaceutical industry
Journal of Computer-Aided Molecular Design - Tập 31 - Trang 301-304 - 2016
Brock Luty, Peter W. Rose
Scientific software engineering is a distinct discipline from both computational chemistry project support and research informatics. A scientific software engineer not only has a deep understanding of the science of drug discovery but also the desire, skills and time to apply good software engineering practices. A good team of scientific software engineers can create a software foundation that is ...... hiện toàn bộ
Computational approaches for predicting mutant protein stability
Journal of Computer-Aided Molecular Design - Tập 30 - Trang 401-412 - 2016
Shweta Kulshreshtha, Vigi Chaudhary, Girish K. Goswami, Nidhi Mathur
Mutations in the protein affect not only the structure of protein, but also its function and stability. Prediction of mutant protein stability with accuracy is desired for uncovering the molecular aspects of diseases and design of novel proteins. Many advanced computational approaches have been developed over the years, to predict the stability and function of a mutated protein. These approaches b...... hiện toàn bộ
Solution conformation by NMR and molecular modeling of three sulfide-free somatostatin octapeptide analogs compared to angiopeptin
Journal of Computer-Aided Molecular Design - Tập 10 - Trang 83-86 - 1996
Philippe Hennig, Eric Raimbaud, Christophe Thurieau, Jean-Paul Volland, André Michel, Jean-Luc Fauchère
The conformation in dimethylsulfoxide of the somatostatin derivative angiopeptin and of three disulfide-free analogs was estimated by two-dimensional nuclear magnetic resonance spectroscopy at room temperature. The resulting 3D molecular graphics were compared and shown to reflect the observed differences in the inhibition of restenosis after rat aorta balloon injury by these octapeptide inhibitor...... 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
Edward E. Hodgkin, Andrew Miller, Mark Whittaker
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
Towards the automatic design of synthetically accessible protein ligands: Peptides, amides and peptidomimetics
Journal of Computer-Aided Molecular Design - Tập 10 - Trang 265-272 - 1996
Hans-Joachim Böhm
The computer program LUDI for the de novo design of protein ligands was extended so that it is now able to take into account the synthetic accessibility of the constructed molecules. As an example, the design of peptides, amides and peptidomimetics using amino acids as building blocks is described. Two new libraries containing natural and non-natural amino acids were constructed for this purpose. ...... hiện toàn bộ
A blind SAMPL6 challenge: insight into the octanol-water partition coefficients of drug-like molecules via a DFT approach
Journal of Computer-Aided Molecular Design - Tập 34 Số 4 - Trang 463-470 - 2020
Evrim Arslan, Basak Koca Fındık, Vi̇ktorya Avi̇yente
Predicting protein–ligand binding modes for CELPP and GC3: workflows and insight
Journal of Computer-Aided Molecular Design - Tập 33 - Trang 367-374 - 2019
Xianjin Xu, Zhiwei Ma, Rui Duan, Xiaoqin Zou
Drug Design Data Resource (D3R) continues to release valuable benchmarking datasets to promote improvement and development of computational methods for new drug discovery. We have developed several methods for protein–ligand binding mode prediction during the participation in the D3R challenges. In the present study, these methods were integrated, automated, and systematically tested using the lar...... hiện toàn bộ
Replacement of steric 6–12 potential-derived interaction energies by atom-based indicator variables in CoMFA leads to models of higher consistency
Journal of Computer-Aided Molecular Design - Tập 9 - Trang 205-212 - 1995
Romano T. Kroemer, Peter Hecht
The steric descriptors commonly used in CoMFA — Lennard-Jones 6–12 potential-derived interaction energies calculated between a probe atom and the molecules under investigation — have been replaced by variables indicating the presence of an atom of a particular molecule in predefined volume elements (cubes) within the region enclosing the ensemble of superimposed molecules. The resulting ‘atom indi...... hiện toàn bộ
5,10-Methylene-5,6,7,8-tetrahydrofolate conformational transitions upon binding to thymidylate synthase: molecular mechanics and continuum solvent studies
Journal of Computer-Aided Molecular Design - - 2005
Adam Jarmuła, Piotr Cieplak, W.R. Montfort
Comparative binding energy analysis of haloalkane dehalogenase substrates: Modelling of enzyme-substrate complexes by molecular docking and quantum mechanical calculations
Journal of Computer-Aided Molecular Design - - 2003
Jan Kmuníček, Michal Boháč, Santos Luengo, Federico Gago, Rebecca C. Wade, Jiří Damborský
We evaluate the applicability of automated molecular docking techniques and quantum mechanical calculations to the construction of a set of structures of enzyme-substrate complexes for use in Comparative binding energy (COMBINE) analysis to obtain 3D structure-activity relationships. The data set studied consists of the complexes of eighteen substrates docked within the active site of haloalkane d...... hiện toàn bộ
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