Journal of Computer-Aided Molecular Design
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Polygalic acid inhibits african swine fever virus polymerase activity: findings from machine learning and in vitro testing
Journal of Computer-Aided Molecular Design - Tập 37 - Trang 453-461 - 2023
African swine fever virus (ASFV), an extremely contagious virus with high mortality rates, causes severe hemorrhagic viral disease in both domestic and wild pigs. Fortunately, ASFV cannot be transmitted from pigs to humans. However, ongoing ASFV outbreaks could have severe economic consequences for global food security. Although ASFV was discovered several years ago, no vaccines or treatments are ......
Structure-based 3D QSAR and design of novel acetylcholinesterase inhibitors
Journal of Computer-Aided Molecular Design - Tập 15 - Trang 395-410 - 2001
The paper describes the construction, validation and application of a structure-based 3D QSAR model of novel acetylcholinesterase (AChE) inhibitors. Initial use was made of four X-ray structures of AChE complexed with small, non-specific inhibitors to create a model of the binding of recently developed aminopyridazine derivatives. Combined automated and manual docking methods were applied to dock ......
The need for scientific software engineering in the pharmaceutical industry
Journal of Computer-Aided Molecular Design - Tập 31 - Trang 301-304 - 2016
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 ......
2D and 3D QSAR studies of diarylpyrimidine HIV-1 reverse transcriptase inhibitors
Journal of Computer-Aided Molecular Design - Tập 22 - Trang 831-841 - 2008
2D and 3D QSAR studies were applied on a set of 28 diarylpyrimidine derivatives to model and understand their HIV-1 reverse transcriptase (RT) inhibitory activities. Special cares were taken to build our set of molecules according to their bioactive conformations which is crucial to elaborate good QSAR models. 2D QSAR was performed using the heuristic method in CODESSA which had led to a linear mo......
Computational approaches for predicting mutant protein stability
Journal of Computer-Aided Molecular Design - Tập 30 - Trang 401-412 - 2016
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......
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
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......
Charge-transfer interactions in the inhibition of MAO-A by phenylisopropylamines – a QSAR study
Journal of Computer-Aided Molecular Design - Tập 16 - Trang 95-103 - 2002
The HOMO energies and the charges on the aromatic carbons of two sets of MAO-A-inhibiting phenylisopropylamines, one containing 4-amino substituents, were calculated by the AM1 method, in order to evaluate the importance of charge-transfer interactions between drug and enzyme. Multiple-linear regressions of the pIC50values on the calculated descriptors were performed with 33 compounds from the two......
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......
In silico rationalization of the structural and physicochemical requirements for photobiological activity in angelicine derivatives and their heteroanalogues
Journal of Computer-Aided Molecular Design - Tập 17 - Trang 53-64 - 2003
In PUVA (Psoralen plus UVA) chemotherapy 8-methoxypsoralen is the most widely used compound, although its efficacy is endowed with undesired side effects. In order to have an evident anti-proliferative activity with a reduced phototoxicity, many linear and angular derivatives have been synthesised. In this paper we describe a QSAR study in which, by means of the neural networks methodology, a usef......
A collaborative environment for developing and validating predictive tools for protein biophysical characteristics
Journal of Computer-Aided Molecular Design - - 2012
The exchange of information between experimentalists and theoreticians is crucial to improving the predictive ability of theoretical methods and hence our understanding of the related biology. However many barriers exist which prevent the flow of information between the two disciplines. Enabling effective collaboration requires that experimentalists can easily apply computational tools to their da......
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