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Towards a critical evaluation of an empirical and volume-based solvation function for ligand docking

Heloisa S. Muniz, Alessandro S. Nascimento, Danilo Roccatano
2017 PLoS ONE  
The evaluation of the solvation energies outstands among the challenges for the modeling of the receptor-ligand interactions, especially in the context of molecular docking where a fast, though accurate  ...  The data provided here is consistent with other empirical solvation models employed in the context of molecular docking and indicates that a good model to account for solvent effects is still a goal to  ...  This method has some advantages for scoring molecular interactions, especially in the context of ligand docking, including the rapid evaluation of the solvent effect in a volume-based approach and the  ... 
doi:10.1371/journal.pone.0174336 pmid:28323889 pmcid:PMC5360343 fatcat:a6hliasifzgyhea4ah3tg4so2m

AutoDock-GIST: Incorporating Thermodynamics of Active-Site Water into Scoring Function for Accurate Protein-Ligand Docking

Shota Uehara, Shigenori Tanaka
2016 Molecules  
This grid map is used as a lookup table during the docking simulation for rapid energy evaluation of ligand conformations.  ...  This grid map is used as a lookup table during the docking simulation for rapid energy evaluation of ligand conformations.  ...  The founding sponsors had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.  ... 
doi:10.3390/molecules21111604 pmid:27886114 fatcat:cle3mpptnrcchjtddh3p45kt4a

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

Garrett M. Morris, Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell, Arthur J. Olson
2009 Journal of Computational Chemistry  
We also report its utility in analysis of covalently bound ligands, using both a grid-based docking method and a modification of the flexible sidechain technique. q  ...  Linear regression analysis of the observed binding constants in terms of a wide variety of structure-derived molecular properties was performed.  ...  of the ligand in the context of the putative active site.  ... 
doi:10.1002/jcc.21256 pmid:19399780 pmcid:PMC2760638 fatcat:shyfdosdtbawbeeglddxcgtj7i

Refinement and Rescoring of Virtual Screening Results

Giulio Rastelli, Luca Pinzi
2019 Frontiers in Chemistry  
BEAR (Binding Estimation After Refinement) was developed as a post-docking processing tool that refines docking poses by means of molecular dynamics (MD) and then rescores the ligands based on more accurate  ...  Therefore, docking results require careful evaluation and further post-docking analyses. In this article, we will overview our approach to post-docking analysis in virtual screenings.  ...  First of all, sampling the conformational space accessible to ligand-target complexes in an induced-fit context is a difficult and target-dependent task.  ... 
doi:10.3389/fchem.2019.00498 pmid:31355188 pmcid:PMC6637856 fatcat:r32i5wuymvdk7dncayuvf3xibi

Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations

Markus A. Lill
2011 Biochemistry  
Different concepts are reviewed that incorporate protein flexibility into protein-ligand docking within the context of these two models.  ...  Conformational changes in the protein that are coupled to ligand binding are described by the biophysical models of induced fit and conformational selection.  ...  FUNDING INFORMATION: This work has in part been supported by the National Institutes of Health (GM085604 and GM092855).  ... 
doi:10.1021/bi2004558 pmid:21678954 pmcid:PMC3172316 fatcat:pazt6siczzbd5jcpxcb7lko554

Ex vivo and in silico Molecular Docking Studies of Aldose Reductase Inhibitory Activity of Apigenin from Morus indica L

Satish Anandan, Murali Mahadevamurthy, Chandra Chandra C, Asna Urooj
2018 Journal of Young Pharmacists  
Materials and Methods: The inhibitory efficacy of API from M. indica was evaluated against ALR in lens tissue of mice by ex vivo and their binding mechanism through molecular docking was carried out by  ...  Results: The API (10-50 µg mL -1 ) concentration exhibited significant inhibition (p ≤ 0.05) of ALR enzyme in a dose dependent manner with IC 50 value of 39.23 µg mL -1 .  ...  Molecular docking of aldose reductase enzyme with API and AG Docking results with the free binding energy, ligand efficiency inhibition constant, Van der wall energy + hydrogen bond + desolving energy,  ... 
doi:10.5530/jyp.2019.11.21 fatcat:7yfl277albhi3ae67rps33ko5i

Virtual screening using the ligand ZINC database for novel lipoxygenase-3 inhibitors

Monika, Janmeet Kour, Kulwinder Singh
2013 Bioinformation  
The analysis resulted in 4319 Lipinski compliant hits which are docked and scored to identify structurally novel ligands that make similar interactions to those of known ligands or may have different interactions  ...  All the ligands were docked within the binding pocket forming interactions with amino acid residues.  ...  Acknowledgment: We would like to extend our heartfelt thanks to Molegro ApS for giving us a fully functional trial version for a period of 30 days during which all the in-silico docking work was carried  ... 
doi:10.6026/97320630009583 pmid:23888100 pmcid:PMC3717187 fatcat:uqvnrdotyvhatg5qgx7ohhkf2a

Practical Considerations in Virtual Screening and Molecular Docking [chapter]

Michael Berry, Burtram Fielding, Junaid Gamieldien
2015 Emerging Trends in Computational Biology, Bioinformatics, and Systems Biology  
Molecular docking algorithms are often calibrated on a training set of experimental ligand-protein complexes and accuracy of these docking programs is often highly dependent on the training set used (  ...  in molecular docking (Rastelli et al., 2010a) .  ... 
doi:10.1016/b978-0-12-802508-6.00027-2 fatcat:64mj5agvwvaxxefzfd4cx3r2zu

Insights from All-Atom Molecular Dynamics Simulations of 40 Nucleosome Chromatin Fiber

Ramu Anandakrishnan, Saeed Izadi, Alexey V. Onufriev
2015 Biophysical Journal  
The present cross-docking study examined dozens of ligands, both agonists and antagonists, in the context of both active and inactive conformations of ER.  ...  on a macromolecule through molecular dynamics (MD) simulations of the macromolecule in an aqueous solution of small molecules.  ... 
doi:10.1016/j.bpj.2014.11.1733 fatcat:x5ustfkgn5dvxcfe3cvqiflb7e

Docking to the Highly Flexible Estrogen Receptor Ligand Binding Domain via Mixed-Resolution Monte Carlo

Sundar Raman Subramanian, Daniel M. Zuckerman
2015 Biophysical Journal  
The present cross-docking study examined dozens of ligands, both agonists and antagonists, in the context of both active and inactive conformations of ER.  ...  on a macromolecule through molecular dynamics (MD) simulations of the macromolecule in an aqueous solution of small molecules.  ... 
doi:10.1016/j.bpj.2014.11.1735 fatcat:u7ly5nnkvfgt5k5ue46ncqubie

Prediction of protein–protein interactions by docking methods

Graham R. Smith, Michael J.E. Sternberg
2002 Current Opinion in Structural Biology  
Abbreviations ACE atomic contact energy BD Brownian dynamics FFT fast Fourier transform GA genetic algorithm MD molecular dynamics NOE nuclear Overhauser enhancement PDB Protein Data Bank rmsd root mean  ...  Several rapid new algorithms have been introduced in the rigid docking problem and promising refinement techniques have been developed, based on modified molecular mechanics force fields and empirical  ...  Similar calculations are used to derive effective potentials between atom types for ligand-protein docking [35] Other terms used in rescoring are electrostatics, hydrogen bonding [36] , desolvation,  ... 
doi:10.1016/s0959-440x(02)00285-3 pmid:11839486 fatcat:bm37bjbbinckjpt7u2i7lhdpwi

Computationally Projecting the Influence of Nucleic Acid on Pathways of Nucleation-Limited Virus Capsid Assembly

Gregory R. Smith, Lu Xie, Russell Schwartz
2015 Biophysical Journal  
The present cross-docking study examined dozens of ligands, both agonists and antagonists, in the context of both active and inactive conformations of ER.  ...  on a macromolecule through molecular dynamics (MD) simulations of the macromolecule in an aqueous solution of small molecules.  ... 
doi:10.1016/j.bpj.2014.11.1734 fatcat:bbgzmktz7jhihczlu5rtiz5bqi

Towards the Simulation of a Complete ATP Synthase: Unravelling the Structural Basis of the Enzyme's Reversible Action

Abhishek Singharoy, Klaus Schulten
2015 Biophysical Journal  
The present cross-docking study examined dozens of ligands, both agonists and antagonists, in the context of both active and inactive conformations of ER.  ...  on a macromolecule through molecular dynamics (MD) simulations of the macromolecule in an aqueous solution of small molecules.  ... 
doi:10.1016/j.bpj.2014.11.1736 fatcat:wm652237avacfmzpu4fbnf65iq

Using Molecular Modelling to Study Interactions Between Molecules with Biological Activity [chapter]

Maria J. R. Yunta
2012 Bioinformatics  
in proteins, docking of small molecules into protein binding sites, proteinprotein docking, and molecular dynamic simulations [see for example Choe & Chang, 2002] .  ...  Molecular modelling methods and their usefulness Molecular recognition is a central phenomenon in biology, for example, with enzymes and their substrates, receptors and their signal inducing ligands, antibodies  ...  in the ease of desolvation of both the ligand and the binding site upon complex formation [Checa et al., 1997] .  ... 
doi:10.5772/54007 fatcat:m3nykutuw5h2tno2mjz6eyb7ki

Virtual screening for novel COX-2 inhibitors using the ZINC database

Kotaprolu Naga Sudha, Mohammed Shakira, Paturi Prasanthi, Nalla Sarika, Ch Narasimha Kumar, Padavala Ajay Babu
2008 Bioinformation  
The analysis resulted in 1042 Lipinski compliant hits which are docked and scored to identify structurally novel ligands that make similar interactions to those of known ligands or may have different interactions  ...  Screening was performed using molecular constraints tool to filter compounds with physico-chemical properties similar to the 6COX bound ligand SC-558.  ...  Docking various ligands to the protein of interest followed by scoring to determine the affinity of binding and to reveal the strength of interaction has become increasingly important in the context of  ... 
doi:10.6026/97320630002325 pmid:18685718 pmcid:PMC2478730 fatcat:lu2iujkrzreubewksgrbqubfhi
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