Comfa and comsia 3dqsar analysis of dmdp derivatives as anti. The predictive ability of comfa and comsia were determined using a test set of 15 imidazole derivatives giving predictive correlation coefficients of 0. Comfa, comsia and eigenvalue analysis eva were performed to study the structural features of 61 diverse dibenzodioxepinone and dibenzodioxocinone analogues to probe cholesteryl ester transfer protein cetp inhibitory activity. Pharm 1st year pharmaceutical chemistry jss college of pharmacy, mysore 2. A 3d grid spacing of 2 a in x, y and z directions and an extension of 4 a beyond the aligned molecules in all directions are used. Illustrations of a comfa molecular interaction and b comsia molecular similarity field contour surfaces depicting steric yellowgreen and electrostatic redblue changes. Comfa and comsia 3d qsar models for a series of cyclic. Comfa, comsia analyses and molecular docking studies nature. Docking, comfa and comsia studies of a series of sulfonamides. Throughput software free download throughput top 4. Modeling study of phenylsulfonylfuroxan derivatives as pgp.
Nov, 2008 a 3dqsar comfa study requires the superimposition of a set of active molecules that are kept in a 3d grid space as the steric and electrostatic fields are calculated at various grid points. The representation of biological activity, partial charge formalism, absolute orientation of the molecules in the grid, and grid spacing were also studied for their effect on the. The 3dqsar models of 15 sulfonamides based on comfa and comsia. Qsar analysis on pfpk7 inhibitors using hqsar, comfa, and. The information obtained from comfa and comsia 3d contour maps can be used for the.
Comparative molecular field analysis comfa hugo kubinyi basf ag, d67056 ludwigshafen, germany 1 introduction. Modeling study of phenylsulfonylfuroxan derivatives as p. Pharmacophore modeling, qsar analysis, comfa, comsia, docking and molecular dynamics simulations, are currently implemented to varying degrees in virtual screening towards. A combined approach of comfa, comsia and hqsar volume. Novel classes of cb2 agonists based on 4oxo1,4dihydroquinoline and 4oxo1,4dihydro1,5, 1,6 and 1,8naphthyridine scaffolds have shown high binding affinity toward cb2. In comfa, steric and electrostatic fields surrounding a set of aligned molecules in a grid box sampled. Comfa and comsia 3d qsar models for a series of some condensed thieno2,3dpyrimidin43hones with antihistaminic h1 activity. Quantitative structureactivity relationship wikipedia. The difference from the comfa results lies in the regionfocused model manifested as an improved comsia model with a q2 of 0. Qsar analysis on pfpk7 inhibitors using hqsar, comfa, and comsia. Comfa and comsia 3d qsar models for a series of cyclic imides with analgesic activity volume. Request pdf qsar analysis on pfpk7 inhibitors using hqsar, comfa, and comsia plasmodium falciparum protein kinase 7 pfpk7 is an important drug target for the development of antimalarial.
The maps obtained by the new comsia approach are superior and easier to interpret whereas the comfa maps denote regions apart from the molecules where interactions with a putative environment are to be expected, the comsia maps highlight those regions within the area occupied by the ligand skeletons that require a particular physicochemical property important for activity. Throughput software free download throughput top 4 download. Tech bioinformatics introduction comfa comparative molecular field analysis is a 3d qsar. The comfa and comsia models presented good internal q 2 0. Unlike comfa and comsia, eva employs a novel alignmentfree descriptor of molecular structure, not field descriptors. Three methods yielded statistically significant models upon assessment of crossvalidation, bootstrapping, and progressive scrambling. Qsar models of cytochrome p450 enzyme 1a2 inhibitors using. Quantitative structureactivity relationship of organosulphur. Both internal and external crossvalidation were conducted to obtain high predictive and satisfactory comfa model q 2 0. Pdf inhibitory activities of flavonoid derivatives against aldose reductase. Urokinasetype plasminogen activator upa, a trypsinlike serine protease, has been implicated in large number of malignancies, tumor cell invasion, angiogenesis and metastasis.
Comfa, comsia and eigenvalue analysis on dibenzodioxepinone. Insight into the structural requirements of urokinasetype. Sep 25, 2012 introduction comfa comparative molecular field analysis is a 3d qsar technique based on data from known active molecules. The following validation techniques were used to calculate the robustness of the developed models. Read development of new comfa and comsia 3dqsar models for antiinflammatory phthalimidecontaining tnf. Quantitative structure activity relationships study of soluble. Throughput software free download throughput top 4 download offers free software downloads for windows, mac, ios and android computers and mobile devices. Comfa and comsia contour maps were then used to analyze the structural features of ligands to. Comfa and comsia analyses on 4oxo1,4dihydroquinoline.
Oct 15, 2006 read development of new comfa and comsia 3dqsar models for antiinflammatory phthalimidecontaining tnf. In comfa, steric and electrostatic fields surrounding a set of aligned molecules in a grid box sampled and correlated with observed activities. The generated models suggested that electrostatic, hydrophobic, and hydrogen bonding interactions play important roles. For the first time, a set of experimentally reported 60 fullerene derivatives were subjected to the 3dqsar comfa and comsia studies. The aim of comfa is to derive a correlation between the biological activity of a set of molecules and their 3d shape, electrostatic and hydrogen bonding characteristics. The align2 database, which included all the active compounds in its alignment, was also subjected to comfa, comsia and hqsar analyses table 5. Quantitative studies on structureorac relationships of anthocyanins from eggplant and radish using 3dqsar pu jinga. The final qsar models as well as the information gathered from 3d contour maps should be useful for the design of novel cyclic imides having improved analgesic. Statistics parameters comfa model comsia model q2 0.
Structurebased optimization of azole antifungal agents by. Quantitative studies on structuredpph scavenging activity. Chapter 5 comfa and comsia investigation of diverse pyrrolidine. The models were further validated following the criteria given by tropsha and roy 31, 32, 37, and were determined to be statistically reliable. In the present study, we have employed the ligandbased drug design technique, 3dqsar, through a comparative molecular field analysis comfa and a comparative molecular. The comfa model b together with the comsia models a and b passed tropshas recommended test for predictive ability, unlike the comfa model a, whose r. The approaches of comfa and comsia are almost similar except for molecular. Removal of two outliers from the initial set of 17 sulfonamide analogs improved the predictability of the models. Introduction to qsar 3d qsar comfa comsia applications case study 3.
Both comfa and comsia studies gave similar results indicating that the steric effects are essential for the activity. As such, the final noncrossvalidated pls analysis model was established from regionfocused descriptors. Pdf androgen receptor has been proved to be effective site for treatment of prostate cancer. Scribd is the worlds largest social reading and publishing site. Comparative molecular similarity indices analysis an overview. Qsar software free download qsar top 4 download offers free software downloads for windows, mac, ios and android computers and mobile devices. The aim of this study is to propose a series of novel.
Comfa, comsia and eigenvalue analysis eva were performed to study the structural features of 61 diverse dibenzodioxepinone and dibenzodioxocinone analogues to probe cholesteryl ester. Comfa and comsia analyses on 4oxo1,4dihydroquinoline and 4. In a continuing effort to develop highly potent azole antifungal agents, the threedimensional quantitative structure. Comfa24 and comsia25,26 descriptors were calculated using the following parameters. Looking for online definition of comfa or what comfa stands for.
Comfa, comsia, hqsar and molecular docking analysis of. For the first time, a set of experimentally reported 60 fullerene derivatives were subjected to the 3dqsarcomfa and comsia studies. Comfa and comsia studies of angiotensin at1 receptor. Quantitative structure activity relationships study of soluble epoxide hydrolase inhibitors using mlr, ann, comfa and comsia methods. Like other regression models, qsar regression models relate a set of predictor variables x to the potency of the response variable y, while classification qsar models relate the predictor variables to a categorical. Eva results unlike comfa and comsia, eva employs a novel alignment free descriptor of molecular. Isbn 9789535103080, pdf isbn 9789535169048, published 20120314 pharmacophore modeling, qsar analysis, comfa, comsia, docking and molecular dynamics simulations, are currently implemented to varying degrees in virtual screening towards discovery of new bioactive hits.
The conformation and alignment of molecules were obtained by a novel method consensus dynamics. Comfa and comsia methods were used for deriving quantitative. A test set of 50 peptides was used to determine the predictive value of the models. Structureactivity relationships based on 3dqsar comfa. The high correlation between the crossvalidatedpredicted and experimental activities of a test set of 12 ligands revealed that the comfa and comsia models were robust r 2 pred comfa 0. Comfa and comsia 3d qsar models for a series of cyclic imides. Comfa deals with electrostatic and steric fields to correlate activity. Two 3dqsar methods comfa and comsia were applied to a set of 38 angiotensin receptor at1 antagonists. Illustrations of a comfa molecular interaction and b comsia molecular similarity field contour surfaces depicting steric yellowgreen and electrostatic redblue changes correlated to activity for a series of 32 elastase inhibitors pk i 2. Quantitative structureactivity relationship models qsar models are regression or classification models used in the chemical and biological sciences and engineering. Chapters comfa and comsia investigation of diverse. Comfa comsia and molecular docking studies of antioxidant. Comfa comsia and molecular docking studies of antioxidantchromone derivatives shravan kumar gunda, shaik mahmood bioinformatics division, osmania university, hyderabad.
Top 4 download periodically updates software information of throughput full versions from the publishers, but some information may be slightly outofdate using warez version, crack, warez passwords, patches, serial numbers, registration codes, key generator, pirate key, keymaker or keygen for throughput license key is illegal. Comfa is listed in the worlds largest and most authoritative dictionary database of abbreviations and acronyms the free. Comsia utilizes seal similarity fileds that also inegrates hydrogen bonding potentials to correlate activity. Introduction comfa comparative molecular field analysis is a 3d qsar technique based on data from known active molecules.
Comfa 3dqsar analysis of hiv1 rt nonnucleoside inhibitors. The most popular qsar methods, comparative molecular field analysis comfa and comparative similarity indices analysis comsia studies incorporate 3d. Comfa comsia and molecular docking studies of antioxidantchromone derivatives shravan kumar gunda, shaik mahmood bioinformatics division, osmania university, hyderabad, andhra pradesh, india500007 corresponding author. Comfa and comsia were employed to generate models to define the specific structural and electrostatic features essential for enhanced binding to the putative gaba. Molecules free fulltext comfa, comsia and eigenvalue. Sep 14, 2017 both internal and external crossvalidation were conducted to obtain high predictive and satisfactory comfa model q 2 0. The aim of this study is to propose a series of novel 60 fullerenebased inhibitors with optimal binding affinity for the hiv1 pr enzyme. Pdf comfa, comsia, hqsar and molecular docking analysis of. Request pdf qsar analysis on pfpk7 inhibitors using hqsar, comfa, and comsia plasmodium falciparum protein kinase 7 pfpk7 is an important drug target for the. Both of the predicted pic 50 in training set and test set were obtained from the comfa model. Pdf comfa and comsia 3d qsar models for a series of some.
Pdf how to generate reliable and predictive comfa models. Modeling study of phenylsulfonylfuroxan derivatives as pgp inhibitors. Comsia section 519,20 and other 3d quantitative similarity. A computational study of comparative molecular fields analysis comfa and comparative molecular similarity indices analysis comsia was performed, in order to identify the key. Insights into the structural requirements of potent. The hydrophobic interactions play a dominant role in peptidemhc molecule binding. Toward the quantitative prediction of tcell epitopes. All the developed models were tested for robustness using various validation techniques. Comfa is listed in the worlds largest and most authoritative dictionary database of abbreviations and acronyms. The align2 database, which included all the active compounds in its alignment, was also subjected to comfa, comsia and. The binding free energies of complexes were calculated using the mmpbsa. Comfa analysis gave a crossvalidated result of q 2 0. Novel classes of cb2 agonists based on 4oxo1,4dihydroquinoline and 4oxo1,4dihydro1,5, 1,6 and 1,8naphthyridine scaffolds have shown high binding affinity toward cb2 receptor and good selectivity over cb1.
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