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
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
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
MENTHOR, a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by substructural, biologic, physical, or geometric properties
Journal of Computer-Aided Molecular Design - Tập 2 - Trang 15-29 - 1988
Yvonne C. Martin, Elizabeth B. Danaher, Catherine S. May, David Weininger
MENTHOR is a database system for the storage and retrieval of three-dimensional coordinate and charge information on molecules as well as of traditional biological and physical properties. Our molecular graphics system retrieves from MENTHOR structural information in individual molecules and receptor map/macromolecular binding site hypotheses. Substructural searches of MENTHOR are used to find sta...... hiện toàn bộ
Modelling and mutation studies on the histamine H1-receptor agonist binding site reveal different binding modes for H1-agonists: Asp116 (TM3) has a constitutive role in receptor stimulation
Journal of Computer-Aided Molecular Design - Tập 9 - Trang 319-330 - 1995
Anton M. ter Laak, Hendrik Timmerman, Rob Leurs, Paul H. J. Nederkoorn, Martine J. Smit, Gabriëlle M. Donné-Op den Kelder
A modelling study has been carried out, investigating the binding of histamine (Hist), 2-methylhistamine (2-MeHist) and 2-phenylhistamine (2-PhHist) at two postulated agonistic binding sites on transmembrane domain 5 (TM5) of the histamine H1-receptor. For this purpose a conformational analysis study was performed on three particular residues of TM5, i.e., Lys200, Thr203 and Asn207, for which a fu...... hiện toàn bộ
Rethinking the applicability domain analysis in QSAR models
Journal of Computer-Aided Molecular Design - Tập 38 - Trang 1-9 - 2024
Jose R. Mora, Edgar A. Marquez, Noel Pérez-Pérez, Ernesto Contreras-Torres, Yunierkis Perez-Castillo, Guillermin Agüero-Chapin, Felix Martinez-Rios, Yovani Marrero-Ponce, Stephen J. Barigye
Notwithstanding the wide adoption of the OECD principles (or best practices) for QSAR modeling, disparities between in silico predictions and experimental results are frequent, suggesting that model predictions are often too optimistic. Of these OECD principles, the applicability domain (AD) estimation has been recognized in several reports in the literature to be one of the most challenging, impl...... hiện toàn bộ
Avalanche for shape and feature-based virtual screening with 3D alignment
Journal of Computer-Aided Molecular Design - Tập 29 Số 11 - Trang 1015-1024 - 2015
David J. Diller, Nancy Connell, William J. Welsh
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