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A self-organizing algorithm for molecular alignment and pharmacophore development

Deepak Bandyopadhyay, Dimitris K. Agrafiotis
2008 Journal of Computational Chemistry  
We present a method for simultaneous three-dimensional (3D) structure generation and pharmacophorebased alignment using a self-organizing algorithm called Stochastic Proximity Embedding (SPE).  ...  Current flexible molecular alignment methods either start from a single low-energy structure for each molecule and tweak bonds or torsion angles, or choose from multiple conformations of each molecule.  ...  This is a novel application of a self-organizing method previously developed for conformational analysis or 3D structure generation.  ... 
doi:10.1002/jcc.20854 pmid:17999384 fatcat:noqsyguw3bcrdm5surk65vgw3e

SitePrint: Three-Dimensional Pharmacophore Descriptors Derived from Protein Binding Sites for Family Based Active Site Analysis, Classification, and Drug Design

James R. Arnold, Keith W. Burdick, Scott C.-H. Pegg, Samuel Toba, Michelle L. Lamb, Irwin D. Kuntz
2004 Journal of chemical information and computer sciences  
provide a direct link to databases of organic molecules.  ...  The SitePrint program generates, aligns, scores, and classifies three-dimensional pharmacophore descriptors, active site grids, and ligand surfaces.  ...  properties using a self-organizing neural net. 12 Protein similarity searches have been conducted using critical points assigned to areas of local curvature on a Connolly surface of the protein. 13  ... 
doi:10.1021/ci049814f pmid:15554689 fatcat:a5s7bdn4i5a2tlii4wdepabx4y

Theoretical and computational approaches to ligand-based drug discovery

Angelo, D. Favia
2011 Frontiers in Bioscience  
Soon after, Richards and colleagues proposed a CoMFA variant, the self-organizing molecular field analysis (SOMFA). However, this was not as popular as CoMFA (22) .  ...  Once developed, a pharmacophore model can be used to parse molecular databases in order to sort the probably inactive compounds from those likely to be active (i.e. those that match the pharmacophore hypothesis  ... 
doi:10.2741/3788 pmid:21196231 fatcat:662k45uccfdedhxds332uresl4

Current computational methods for predicting protein interactions of natural products

Aurélien F.A. Moumbock, Jianyu Li, Pankaj Mishra, Mingjie Gao, Stefan Günther
2019 Computational and Structural Biotechnology Journal  
As a result, computational predictions are preferentially used in the first instance for NP profiling, prior to experimental validations.  ...  Computational DTI prediction methods have the potential to significantly advance the discovery and development of novel selective drugs exhibiting minimal side effects.  ...  map-based prediction of drug equivalence relationships) utilizing the concept of unsupervised self-organizing map (SOM) algorithm applied in combination with pharmacophore feature representations for  ... 
doi:10.1016/j.csbj.2019.08.008 pmid:31762960 pmcid:PMC6861622 fatcat:ml6p54iqjvh5lh7nzew2xhm3oe

Computational Drug Repurposing Resources and Approaches for Discovering Novel Antifungal Drugs against Candida albicans N-Myristoyl Transferase

Afzal Hussain, Chandan Kumar Verma
2021 Journal of Pure and Applied Microbiology  
This review intends to utilize advanced bioinformatics technologies such as Molecular docking, Scaffold hopping, Virtual screening, Pharmacophore modeling, Molecular dynamics (MD) simulation for the development  ...  For reducing its infection, limited drugs are existing such as caspofungin, fluconazole, terbinafine, and amphotericin B, etc. which contain unlikable side effects and also toxic.  ...  The ligands have been divided into training and test for alignment and generating a pharmacophore model, presented in Fig. 10 .  ... 
doi:10.22207/jpam.15.2.49 fatcat:4pizyrkscbdnrfxzueu7fu2nhm


Sneha Rai, UTKARSH RAJ, Swapnil Tichkule, Himansu Kumar, Sonali Mishra, Neeti Sharma, Richa Buddham, Dhwani Raghav, Pritish Kumar Varadwaj
2015 International Journal for Computational Biology  
The major approach of structure based drug designing is Molecular docking, a method based on several sampling algorithms and scoring functions.  ...  All the candidate leads obtained by various drug designing method need to satisfy ADMET properties for its development as a drug.  ...  A Pharmacophore elucidation algorithm is use to generate pharmacophore models after the alignment step is completed.  ... 
doi:10.34040/ijcb.5.1.2015.71 fatcat:5qkg22mhzfc5reyuuvnvfunkwi

Neural networks and genetic algorithms in drug design

2001 Drug Discovery Today  
prediction, locating proteincoding regions in DNA sequences, 3D structure alignment, pharmacophore perception, docking of ligands to receptors, automated generation of small organic compounds, and the  ...  A variety of artificial neural network methods have been developed. Here, we single out some of the more prominent methods. For a list of online resources for neural networks, see Box 1.  ...  (COMSA), developed by Polanski and Gasteiger, and further elaborated by Polanski and Walczak 12 , combines the mapping of the mean electrostatic potential on the molecular surface (by a Kohonen self-organizing  ... 
doi:10.1016/s1359-6446(01)00173-8 fatcat:5jt3r4bgfvbe5b6phd4lidln4a

Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback?

Andrzej Bak
2021 International Journal of Molecular Sciences  
In fact, a myriad of 4D-QSAR methods have been implemented and applied practically for a diverse range of molecules.  ...  of the 'mainstream' algorithms.  ...  Acknowledgments: Special thanks to all 4D-QSAR developers. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms22105212 pmid:34069090 pmcid:PMC8156896 fatcat:rzktyhk6tzaa3ifiqhg6hbyjpa

Other Related Techniques [chapter]

Kunal Roy, Supratik Kar, Rudra Narayan Das
2015 Understanding the Basics of QSAR for Applications in Pharmaceutical Sciences and Risk Assessment  
of ligand flexibility, proficient molecular alignment algorithms, and more precise model optimization.  ...  Expert system techniques are adopted Table 10 .2 10 Software and programs for pharmacophore modeling Ligand-based methods Software Conformational analysis algorithm Molecular alignment Significant  ... 
doi:10.1016/b978-0-12-801505-6.00010-7 fatcat:s3cwmvwklngdfdcwjb4vnqejci

Trend of Multi-Scale QSAR in Drug Design

Lian Sheng Qiao, Yi-Lian Cai, Yu-Su He, Lu-Di Jiang, Xiao-Qian Huo, Yan-Ling Zhang
2014 Asian Journal of Chemistry  
activity are used to construct correlation function model by suitable algorithm.  ...  Afterwards, statistical methods are applied for internal validation of the model. Finally, the test set is used for external test of the model.  ...  Also, that was the reason for the atom-based alignment was developed. 3D atom-based QSAR is a combination of pharmacophore and 3D-QSAR methods.  ... 
doi:10.14233/ajchem.2014.18490 fatcat:hmezfn5mfvbrpfiftqvhfa57km

Development of modulators of multidrug resistance: A pharmacoinformatic approach

G. F. Ecker, Peter Chiba
2004 Pure and Applied Chemistry  
Inhibition of drug efflux pumps such as P-glycoprotein represents a versatile approach for overcoming multidrug resistance in tumor therapy.  ...  These include 2D-and 3D-QSAR studies, artificial neural networks, and photoaffinity labeling studies.  ...  Self-organizing maps for lead identification Artificial neural networks represent a versatile tool for modeling abstract and complex relationships.  ... 
doi:10.1351/pac200476050997 fatcat:6wsc63oclrgkxeavvi27xr4m7e

Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) Studies on α1A-Adrenergic Receptor Antagonists Based on Pharmacophore Molecular Alignment

Xin Zhao, Minsheng Chen, Biyun Huang, Hong Ji, Mu Yuan
2011 International Journal of Molecular Sciences  
32 ligands using pharmacophore-based molecular alignment.  ...  Our study serves as a guide for further experimental investigations on the synthesis of new compounds.  ...  This work was financial supported by the Science and Technology Research and Development Plan Project of Guangzhou (No. 2009A1-E011-7), China.  ... 
doi:10.3390/ijms12107022 pmid:22072933 pmcid:PMC3211024 fatcat:cgqmjgl3yfaxrorwqhxb5nbu3i

Advances in diversity profiling and combinatorial series design [chapter]

Dimitris K. Agrafiotis, James C. Myslik, F. Raymond Salemme
1999 Annual Reports in Combinatorial Chemistry and Molecular Diversity  
, using molecular diversity as a means to design and prioritize experiments.  ...  'I understand rabbi, it was a stupid question.' 'Not only that, but you are stupid, your wife's a meeskeit, and if you don't get off my foot you are excommunicated.' Woody Allen, Getting Even.  ...  Self-organized non-linear mapping is a variant of Sammon's original algorithm that was developed by Agrafiotis [44, 50] and is based on a selforganization principle reminiscent of Kohonen's SOM training  ... 
doi:10.1007/978-94-017-0735-0_9 fatcat:gyw3bjjowracte76rdbnaor5hi

Insight into the Structural Determinants of Imidazole Scaffold-Based Derivatives as TNF-α Release Inhibitors by in Silico Explorations

Yuan Wang, Mingwei Wu, Chunzhi Ai, Yonghua Wang
2015 International Journal of Molecular Sciences  
By using the distance comparison technique (DISCOtech), comparative molecular field analysis (CoMFA), and comparative molecular similarity index analysis (CoMSIA) methods, the pharmacophore models and  ...  All these models have extended the understanding of imidazole-based compounds in the structure-activity relationship, and are useful for rational design and screening of novel 2-thioimidazole-based TNF-α  ...  Acknowledgments Thanks for the support given by the high-performance computing platform of Northwest A&F (Agriculture and Forestry) University. This work is supported by grants from Northwest A&F  ... 
doi:10.3390/ijms160920118 pmid:26307982 pmcid:PMC4613192 fatcat:hu5sj733vzf4pgrzth5zx5x7gq

Pharmacophore-based discovery of ligands for drug transporters

Cheng Chang, Sean Ekins, Praveen Bahadduri, Peter W. Swaan
2006 Advanced Drug Delivery Reviews  
The ability to identify ligands for drug transporters is an important step in drug discovery and development.  ...  Various implementations of pharmacophore model generation, database compilation and flexible screening algorithms are also introduced.  ...  We are grateful for the considerable efforts of John Ohrn and Carrie Estes (Accelrys, San Diego, CA) in making Catalyst available to us.  ... 
doi:10.1016/j.addr.2006.09.006 pmid:17097188 pmcid:PMC1773055 fatcat:dvhdgppf3nbdbifobkrtofasmm
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