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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