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Molecular Docking Screens Using Comparative Models of Proteins

Hao Fan, John J. Irwin, Benjamin M. Webb, Gerhard Klebe, Brian K. Shoichet, Andrej Sali
2009 Journal of Chemical Information and Modeling  
We suggest how to exploit comparative models for molecular screens, based on docking against a wide range of crystallographic structures and comparative models with known ligands.  ...  Investigators have nevertheless been cautious about using comparative models for ligand discovery because of concerns about model errors.  ...  In conclusion, these results suggest techniques to best exploit comparative models in molecular docking screens: Whether one or multiple templates are available, comparative models are best used via consensus  ... 
doi:10.1021/ci9003706 pmid:19845314 pmcid:PMC2790034 fatcat:nyvbkezyezhzlhcbposzdfth54

RNA aptamer evaluation using Comparative Molecular Interaction Profile Analysis system

Y. Hayashi, S. Takahashi, K. Sakaguchi, N. Iwata, M. Kobayashi
2003 Nucleic Acids Symposium Series  
By using 3-bases RNA fragment, the system can use computational molecular docking results to help for RNA aptamer screening.  ...  In this paper, we introduce a system named Comparative Molecular Interaction Profile Analysis system (CoMIPA) that utilizes virtual docking study for comprehensive analysis of molecular interactions.  ...  By using 3-bases RNA fragment, the system can use computational molecular docking results to help for RNA aptamer screening.  ... 
doi:10.1093/nass/3.1.197 fatcat:apwp6c26wjgzdgnyoqtgdajcve

Progress in molecular docking

Jiyu Fan, Ailing Fu, Le Zhang
2019 Quantitative Biology  
Therefore, this review introduces the basic theories of molecular docking and compares the commonly used docking software.  ...  Also, it compares the commonly used docking applications and recommends which research areas are suitable for them.  ...  This article is a review article and does not contain any studies with human or animal subjects performed by any of the authors.  ... 
doi:10.1007/s40484-019-0172-y fatcat:dtserj22xngfpnvv2pmzkajkza

Virtual Screening: A Fast Tool for Drug Design

Vivek Vyas
2008 Scientia Pharmaceutica  
Ligand based screening techniques mainly focus on comparing molecular similarity analyses of compounds with known and unknown moiety, regardless of the methods of the used algorithm.  ...  Docking is a computational tool of structure based drug design to predict protein ligand interaction geometries and binding affinities.  ...  Comparative modeling based on homologous proteins of known structure can generate such a model.  ... 
doi:10.3797/scipharm.0803-03 fatcat:tti5ecuy4vg5paj5fraqm2gakm

Structure-Based Pharmacophore Modeling, Virtual Screening and Molecular docking for the Treatment of ESR1 Mutations in Breast Cancer

Anum Munir, Shumaila Azam, Azhar Mehmood
2016 Drug Designing: Open Access  
compounds were docked with ESR1 proteins.  ...  Compounds that fulfill all properties of Lipinski rule of five were docked with proteins, 3 compounds demonstrated ideal docking results.  ...  Muhammad Haseeb from Capital University of Sciences and Technology, who provided beneficial information to conduct research work.  ... 
doi:10.4172/2169-0138.1000137 fatcat:5ybfvfzjorgunazrdbryttgswm

Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening

Hongying Du, Jeffrey R. Brender, Jian Zhang, Yang Zhang
2015 Methods  
These results suggest that the combination of structure-based docking and advanced protein structure modeling methods should be a valuable approach to the large-scale drug screening and discovery studies  ...  which achieve comparable enrichment rates to using the experimental bound crystal structure in the majority of the cases studied.  ...  Acknowledgement The project is supported in part by the National Institute of General Medical Sciences (GM083107, GM084222).  ... 
doi:10.1016/j.ymeth.2014.08.017 pmid:25220914 pmcid:PMC4431978 fatcat:va2wkkhi5ngj5cfqbyzh2ssgra

Building a virtual ligand screening pipeline using free software: a survey

Enrico Glaab
2015 Briefings in Bioinformatics  
SWISS-MODEL Repository [9] 3D protein models from homology modelling 3.2 million models http://swissmodel.expasy.org/repository/ Protein Model Portal (PMP) [10] Integration of modelled structures from  ...  He has set up and manages the Institute's virtual screening pipeline and works on drug target prioritization using omics data, screening based on receptors and ligands and biological applications of machine  ...  If no suitable experimental structure for molecular docking simulations can be identified for a chosen target protein, a binding site structural model may alternatively be derived from comparative modelling  ... 
doi:10.1093/bib/bbv037 pmid:26094053 pmcid:PMC4793892 fatcat:jwhqn6n3hnh4pjtcmbgv4jq6ia

A Structural Model of Glycosylated Neuraminidase Based on Molecular Dynamics Simulations for Virtual Inhibitor Screening Against Influenza Virus

Young-Jin Choi, Chan-Ho Kwon, Eun-Ae Cho, In-Cheol Kang, Hyun-Ja Jeong, Sung-Jun Park, Karp-Joo Jeong, Tak Hur, Seun-Ho Jung
2012 Bulletin of the Korean Chemical Society (Print)  
This work was supported by Academic Research Grant of Hoseo University in 2008 (2008-0126).  ...  The structural properties of these glycosylated NA protein models were compared with the unglycosylated model using 30-ns of MD simulations.  ...  Binding characteristics of inhibitor for the alternative MD models of NA protein by glycosylation was analyzed using molecular docking simulations of oseltamivir onto the different NA structures.  ... 
doi:10.5012/bkcs.2012.33.3.1059 fatcat:howc54njwbgwlmqo7nduzuelsm

A Molecular Dynamics-Shared Pharmacophore Approach to Boost Early-Enrichment Virtual Screening: A Case Study on Peroxisome Proliferator-Activated Receptor α

Ugo Perricone, Marcus Wieder, Thomas Seidel, Thierry Langer, Alessandro Padova, Anna Maria Almerico, Marco Tutone
2017 ChemMedChem  
This was done in order to compare the ranking of molecular docking with that of pharmacophore modelling.  ...  Twoo ft he most frequently used approaches in the field of structurebased computer-aided drug design are molecular docking and pharmacophore modelling and screening.B oth virtual screening approaches aim  ... 
doi:10.1002/cmdc.201600526 pmid:28135036 fatcat:onc6iolnyvfndjhs2sunui5iqq

A ClpP protein model as tuberculosis target for screening marine compounds

Abhilasha Tiwari, Smita Gupta, Shipra Srivastava, Rajeev Srivastava, Anil Kumar Rawat
2010 Bioinformation  
Stable model was further used for virtual screening against marine derived bioactive compound database through molecular docking studies using AutoDock 3.05.  ...  The computed model's energy was minimized and validated using PROCHECK to obtain a stable model structure and is submitted in Protein Model Database (PMDB-ID: PM0075741).  ...  Virtual screening Virtual screening of the entire 186 marine compounds of MCDB [3,4] against ClpP protein structure, determined by comparative homology modeling, were done using molecular docking program  ... 
doi:10.6026/97320630004405 pmid:20975890 pmcid:PMC2951636 fatcat:dhylqfrc5nhu3kglyad55beoya

Computer-Based Methods of Inhibitor Prediction [chapter]

Silvana Giuliatti
2013 An Integrated View of the Molecular Recognition and Toxinology - From Analytical Procedures to Biomedical Applications  
Author details Silvana Giuliatti * Address all correspondence to: silvana@fmrp.usp Faculty of Medicine of Ribeirão Preto -University of São Paulo, Brazil An Integrated View of the Molecular Recognition  ...  Molecular Docking One application of molecular docking is virtual screening, in which a library of compounds is compared to one or more targets, thereby providing an analysis of compounds ranked by potential  ...  Molecular docking completes the structure-based virtual screening.  ... 
doi:10.5772/52334 fatcat:3wy4knraxvdthjpldxly6rcof4

Identification and In-silico Prediction of Hermetiaillucens Larval Protein That Inhibits the Progression of Cervical Cancer

2020 International Journal of Engineering and Advanced Technology  
The molecular docking of the peptides with onco-proteins has been predicted and virtually screened based on RMSD values.  ...  To screen the best active potential molecule for cancer treatment the Molecular dynamics of docked protein-peptide structures were administered.  ...  used for molecular docking.  ... 
doi:10.35940/ijeat.c5715.029320 fatcat:ripkj4yj6ffplnuilw2fdi742m

Structural elucidation of SrtA enzyme in Enterococcus faecalis: an emphasis on screening of potential inhibitors against the biofilm formation

Chandrabose Selvaraj, Jeyachandran Sivakamavalli, Baskaralingam Vaseeharan, Poonam Singh, Sanjeev Kumar Singh
2014 Molecular Biosystems  
Present work is an inclusive report of structural elucidation in SrtA and screening of potent inhibitors targeting E. faecalis through computational and experimental methodologies.  ...  The quality of average structure is visualized and compared with initial model structure and it shows model protein structure is refined based on molecular dynamics simulations.  ...  Because the homology model protein has neutral charges, which is not compact for docking and other molecular modeling techniques.  ... 
doi:10.1039/c3mb70613c pmid:24718729 fatcat:r3h25o63z5cpbi47teq55yc6wm

In Silico Screening of Isocitrate Lyase for Novel Anti-Buruli Ulcer Natural Products Originating from Africa

Samuel Kwofie, Bismark Dankwa, Emmanuel Odame, Francis Agamah, Lady Doe, Joshua Teye, Odame Agyapong, Whelton Miller, Lydia Mosi, Michael Wilson
2018 Molecules  
A library consisting of 885 compounds retrieved from the AfroDb database was virtually screened against the validated ICL model using AutoDock Vina.  ...  The three-dimensional (3D) structure of Isocitrate lyase (ICL) of Mycobacterium ulcerans was generated using homology modeling and was further scrutinized with molecular dynamics simulations.  ...  Conflicts of Interest: The authors declare no conflicts of interest.  ... 
doi:10.3390/molecules23071550 pmid:29954088 fatcat:ftpt2wbrebhnhoc74otval6pgu

MOLECULAR DOCKING SOFTWARE'S APPLICATIONS AND BASIC CHALLENGES FACED: A REVIEW

Shalini K Sawhney, Monika Singh
2020 International Research Journal of Pharmacy  
There are three types of Docking: Protein-Protein Docking, Protein-Ligand Docking and Protein-Protein and Protein-Ligand docking.  ...  Given the biological and pharmaceutical importance of molecular docking, considerable efforts have been directed towards improving the methods used to calculate docking.  ...  ACKNOWLEDGEMENT Authors thank ITS College of Pharmacy, Muradnagar, Ghaziabad, India for the support to publish the work.  ... 
doi:10.7897/2230-8407.110213 fatcat:pfpmnxajwbhebooehmk5atkxli
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