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Topic: Pharmacophore

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	Overview of Pharmacophore Applications in MOE (Site not responding. Last check: 2007-11-03)
		The pharmacophore was then applied to a second database (the "search" database) of 1957 compounds of unknown inhibition activity to search for possible new candidates.
		Prior to searching, pharmacophore annotations were calculated for all molecules in the test database using the Pharmacophore Preprocessor, a utility that is also integrated into the Pharmacophore Search application.
		With the flavone pharmacophore query, 20 hit molecules were obtained, of which 1 was non-flavonoid (coumesterol), and 19 were flavonoids; none were steroids.
	www.chemcomp.com /Journal_of_CCG/Articles/ph4.htm (1989 words)

	jcadd
		The earliest appearance of the term pharmacophore in the original literature that I have found is the last sentence on p.
		It appears that Kier first articulated the modern concept of the pharmacophore in his chapter 'Receptor Mapping using MO Theory', proceedings of a 1968 symposium published in 1970 as the book "Fundamental Concepts in drug-receptor interactions" (Danielli, Moran and Triggle, eds.).
		Pharmacophores are shown for both muscarinic and dopamine receptors, but that term was not used - they were called models in that paper.
	www.mindspring.com /~vandrie/jcadd.htm (2349 words)

	Pharmacophore discovery for ACE (angiotensin-converting enzyme) inhibition (OxUni) (Site not responding. Last check: 2007-11-03)
		A pharmacophore for a given activity (such as ACE-inhibition) is a structural property that causes the activity.
		Pharmacophores are typically described in terms of types of atoms (e.g., hydrogen donors) or functional groups and the pairwise distances among them.
		This pharmacophore appears in all 28 molecules at the 0.75 and 1 Angstrom levels, and 27 molecules at the 0.5 Angstrom level.
	www-ai.ijs.si /~ilpnet/apps/pdai.html (347 words)

	Pharmacophore Identification and the Unknown Receptor Problem (Site not responding. Last check: 2007-11-03)
		A pharmacophore is a specific, three dimensional map of biological properties common to all active conformations of a set of ligands which exhibit a particular activity.
		The pharmacophore, a 3 to 5 point abstraction, must be congruent to the functional components of at least one active conformation for each inhibitor, in order to represent the entire set.
		The problem of pharmacophore identification is to generate the pharmacophore from structural data describing ligands and their interaction with the receptor.
	cnx.org /content/m11538/latest (1802 words)

	ChemBridge - Pharmacophore Library
		With 60,000 compounds in stock (to be extended to 100,000 by December, 2003), represents a substantial and growing component of the ChemBridge Corporate Compound Collection for Screening, available on a non-exclusive basis.
		ChemBridge Corporation has designed the PHARMACophore library in response to the emerging market's need for chemically sophisticated, novel combinatorial libraries with biologically relevant diversity, which are comprised of lead/drug-like, pure and quality proven individual compounds.
		Biologically relevant 3D pharmacophore/ 2D diversity, and drug-like properties of compounds are all addressed.
	www.chembridge.com /pharmacophore_library.html (372 words)

	HIV-1 integrase pharmacophore: discovery of inhibitors through three-dimensional database searching.
		Out of the open, nonproprietary part of this database, comprising approximately 200000 compounds, 267 structures were found to match the pharmacophore in at least one conformation, and 60 of those were tested in an in vitro assay against HIV-1 IN.
		An automated pharmacophore identification procedure performed on this set of compounds provided additional support for the importance of this pharmacophore for binding of inhibitors to IN and hinted at a possible second pharmacophore.
		The role of aromatic moieties in the binding of ligands to HIV-1 IN through interactions with divalent metal cations, which are known to be necessary for activity of the enzyme, was explored in ab initio calculations.
	www.aegis.com /aidsline/1997/jul/M9772047.html (468 words)

	Pharmacophore contents
		Perceiving a pharmacophore is the most important first step towards understanding the interaction between a receptor and a ligand.
		It starts with a contribution from Sandra Handschuh and Johann Gasteiger in Chapter 23 entitled “Pharmacophores Derived from the 3D Substructure Perception.” Isaac Bersuker, Süleyman Bahçeci, and James Boggs present “The Electron-Conformational Method of Identification of Pharmacophore and Anti-Pharmacophore Shielding” a novel perspective towards pharmacophore identification.
		Contrast this to the first use of the term “pharmacophore.” It was first used in early 1900s as Peter Gund explains in Chapter 1; however, the meaning of the definition remained remarkably unperturbed during its close to 90 years of existence.
	www.iul-press.us /Books/BBT02-Pharmacophore/content-pha.html (1571 words)

	Substrate specificity of the ileal and the hepatic Na+/bile acid cotransporters of the rabbit. II. A reliable 3D QSAR ... (Site not responding. Last check: 2007-11-03)
		Pharmacophore for the ileal Na /bile acid cotransporter.
		Mapping of cholyltaurine onto the pharmacophore model by using 12-OH as hydrogen bond donor.
		Mapping of cholyltaurine onto the pharmacophore model by using 7-OH as hydrogen bond donor.
	www.jlr.org /cgi/content/full/40/12/2158 (4506 words)

	[No title]
		The generation of the pharmacophores is first described, then exploring conformations which might exhibit a pharmacophore of interest and finally scoring the resulting solutions or hits.
		The pharmacophore generation stage thus provides a list of pharmacophores that are possibly exhibited by the ligand molecule and the atoms in the ligand that define those pharmacophores.
		The geometry of conformers which exhibit the pharmacophore and score less than a cutoff (by default 1000.) are refined using a SIMPLEX minimiser to adjust the torsion angles, x,y,z orientation and position of the molecule in the site.
	www.treweren.com /think1a.htm (2424 words)

	[No title] (Site not responding. Last check: 2007-11-03)
		Catalyst calculates a conformational model for each molecule, creates initial pharmacophores that are common among the active compounds but not among the inactive compounds, and optimizes the pharmacophores using simulated annealing.
		Each pharmacophore is scored using a cost function that accounts for its complexity, the deviation from ideal chemical weights for each chemical feature, and the differences between the predicted and measured activities.
		This used the concepts of pharmacophore fingerprints or keys which have also been used to identify pharmacophores which may be associated with activity.
	www.lib.uchicago.edu /~atbrooks/CINF/abstracts_217.html (10255 words)

	Pharmacophore Design (Site not responding. Last check: 2007-11-03)
		ILP has been successfully applied to forming pharmacophores and quantitative structure activity relationships (QSARs) when there is no knowledge of the target protein structure [5,6].
		We have also used ILP in a novel 4D-QSAR approach to pharmacophore mapping and QSAR analysis using information from a series of ligand-protein complexes and their associated biological activities [7].
		New work involves the use of GRID probes to characterize the pharmacophore points found by ILP, such that each point can be described by a particular GRID probe with an associated energy of interaction.
	biop.ox.ac.uk /www/lj2001/watson/watson_02.html (442 words)

	Energy Citations Database (ECD) - Energy and Energy-Related Bibliographic Citations
		The development of ''dynamic'' pharmacophore models is a new method that accounts for the inherent flexibility of the active site and aims to reduce the entropic penalties associated with binding a ligand.
		All protein conformations from the MD are overlaid, and conserved binding regions for the probe molecules are identified.
		Also, a ''static'' pharmacophore model was determined in the standard fashion, using a single crystal structure.
	www.osti.gov /energycitations/product.biblio.jsp?osti_id=15010435 (416 words)

	THINK Release Notes v1.23
		The introduction of fuzzy pharmacophores is designed to handle the tolerances on the exact positions of the centres (atoms) that define a pharmacophore, which affects the distances between the atoms.
		Since the pharmacophore tolerance is applied independently to each of the distances within a pharmacophore, the number of fractional pharmacophores created increases dramatically as the number of centres, and hence the number of distances, rises.
		It is also recommended that all salts are removed from the structures before the pharmacophores are calculated, since salts may contain centres (eg oxygen atoms) which would lead to the creation of additional pharmacophores partially or wholly outside the molecule that is to be used in the data analysis.
	www.treweren.com /manuals/rn123.htm (6309 words)

	3-D searching by Pharmacophore Tutorial
		The definition of a pharmacophore is the minimum functionality a molecule has to contain in order to exhibit activity.
		For a series of derivatives, the molecules usually have much in common and to derive the true minimum pharmacophore, structurally diverse active molecules are required.
		So this pharmacophore is less stringent than the first we used (we removed a feature).
	www.cmbi.ru.nl /edu/bioinf4/3D-Prac/pharm.shtml (898 words)

	Three-Dimensional Quantitative Structure-Activity Relationship for Inhibition of Human Ether-a-Go-Go-Related Gene ... (Site not responding. Last check: 2007-11-03)
		by a pharmacophore for the inhibition of this potassium
		A General Catalyst pharmacophore was generated using 15 molecules with literature data (Table 2).
		To further test the validity of the pharmacophore one approach is to randomize the structures and activity to assess whether
	jpet.aspetjournals.org /cgi/content/full/301/2/427 (4495 words)

	Pharmacophore Perception, Development and use in Drug Design
		The term "pharmacophore" was first used in the early 1900s, and since that time has become the underlying tenet of drug design.
		There is a historical perspective that describes how pharmacophores were described in the past, what types of approaches have been tried, and which ones worked best under what circumstances.
		This chaper is a historical overview of the "Evolution of the Pharmacophore Concept in Pharmaceutical Research", from man's earliest beginnings to the present time.
	www.balbes.com /articles/osmanreview.html (1311 words)

	Selected Publications
		A concept introduced by Ehrlich at the turn of the century, this is the critical three-dimensional arrangement of molecular fragments (or distribution of electron density) that is recognized by the receptor and, in the case of agonists, causes subsequent activation of the receptor upon binding.
		In other words, some parts of the molecule are essential for interaction, and they must be capable of asuming a particular three-dimensional pattern that is complementary to the receptor in order to interact favorably.
		Derivation of a Three-Dimensional Pharmacophore Model of Substance P Antagonists Bound to the Neurokinin-1 Receptor.
	www.cmd.wustl.edu /Publications.htm (4037 words)

	MRI ABSTRACT (Site not responding. Last check: 2007-11-03)
		To provide further evidence that the 3D pharmacophore developed embodied common requirements for receptor recognition, a pharmacophore analysis was performed for agonists, inverse agonists and antagonists separately.
		Each of the resulting pharmacophores contained the same five moieties at comparable distances to those found for the pharmacophore generated using all of them together.
		Second, four benzodiazepine receptor ligands known to have an effect at the sedation endpoint, but not used in the pharmacophore development were found to satisfy the requirements of this pharmacophore.
	www.molres.org /abs/2000e_dlh.html (344 words)

	Inte:Ligand: Your partner for in-silico drug discovery
		The 3D pharmacophore on the right illustrates the chemical features shared between three inhibitors of Cyclin Dependent Kinase 2 (CDK2), an important anti-cancer target.
		The pharmacophore model as well as the alignment with the inhibitors were created and visualized using Inte:Ligand's brand new program LigandScout.
		After four months of public beta testing, Inte:Ligand's 3D pharmacophore modeling tool LigandScout has reached productivity status and is publicly available to researchers.
	www.inteligand.com (170 words)

	A common pharmacophore for cytotoxic natural products that stabilize microtubules -- Ojima et al. 96 (8): 4256 -- ...
		The pharmacophore succeeds in explaining the substantial structure-activity
		An important triumph of the proposed common pharmacophore is that it accommodates the nonessential nature of the C12-C13 epoxide
		Prior preliminary studies on the common pharmacophores for nonataxel, paclitaxel, epothilones, and discodermolide have been
	www.pnas.org /cgi/content/full/96/8/4256 (3555 words)

	The National Cancer Institute 3D structure database
		In many cases the important points of interaction between a drug and its target can be represented by a 3D arrangement of a small number of atoms.
		Such a group of atoms is called a pharmacophore.
		The pharmacophore can be used to seach 3D databases and drugs that match the pharmacophore could have similar biological activity, but have very different patterns of atomic connections.
	dtp.nci.nih.gov /docs/3d_database/dis3d.html (318 words)

	Elucidation of Vasoactive Intestinal Peptide Pharmacophore for VPAC1 Receptors in Human, Rat, and Guinea Pig -- ...
		Elucidation of Vasoactive Intestinal Peptide Pharmacophore for VPAC
		Therefore, the goal of the present study was to determine the VIP pharmacophore for the VPAC
		Because guinea pigs or rats are frequently used for in vivo studies and it is reported the VIP receptor pharmacophore is the
	jpet.aspetjournals.org /cgi/content/full/301/1/37 (6949 words)

	Pharmacophore Perception, Development and Use in Drug Design
		The book entitiled Pharmacophore Perception, Development, and Use in Drug Design, which has been just released [1], is the first monograph dedicated to the topic of the pharmacophore.
		The first chapter stes the tone for the volume by giving a very interesting account of the evolution of the concepts of pharmacophore and related terms such as chromophore, chemotherapy (p.6), topological patterns of molecules, drug-receptor interaction (p.7), ligand-receptor binding, topographic patterns (p.8) and so on.
		Predicting Drug-Drug Interactions in Silico using Pharmacophores: A Paradigm for the Next Millenium.
	www.mdpi.org /molecules/html/50700987.htm (434 words)

	[No title]
		Go to the Pharamacophore Mapping panel." STRING -i c2scsAlertRS3 -t "Error: No pharmacophore distance pairs are specifed.\nGo to the Pharamacophore Mapping panel." STRING -i c2scsAlertRS4 -t "Nothing to do.
		There are no other pharmacophores\ndefined to search using the prior pharmacophore." STRING -i c2scsAlertRS5 -t "Could not find movable torsions for all specified search models." STRING -i c2scsAlertDPL1 -t "Warning: New pharmacophore has a different number of atoms.
		Reload this pharmacophore." STRING -i c2scsAlertRPS5 -t "Error: The number of pharacophore atoms has changed from that in the\nfile %s (%i).
	www.ualberta.ca /dept/chemeng/package/CERIUS/cerius2_4.2MS/db/cfg.gdf (741 words)

	Products
		Screen is a comprehensive HTS suite in JChem, which works with files and structure databases and features various models for the similarity analysis of molecules and pharmacophore hypotheses.
		The pharmacophore mapping tool offers customizable pharmacophore models as well as an optimizer to find the "best" screening metrics and parameter sets.
		JKlustor is a tool of JChem for clustering, diversity calculations, and library comparisons based on molecular fingerprints and other descriptors.
	www.chemaxon.com /products.html (756 words)

	RAPID: Randomized Pharmacophore Identification for Drug Design - Finn, Kavraki, Latombe, Motwani, Shelton, ... (Site not responding. Last check: 2007-11-03)
		Please let us know if you encounter any data corruptions.
		This document uses CoBlitz to cache paper downloads.
		Such invariants of chemically distinct molecules are useful for computational chemists since they may represent candidate pharmacophores.
	citeseer.ist.psu.edu /78260.html (411 words)

	Combinatorial Chemistry - index (Site not responding. Last check: 2007-11-03)
		DAC in-licences compound intellectual property identified using Evotec’s proprietary fragment screening platform.
		Comparison of Pharmacophore Searching Methods for Potential Inhibitors of Tyrosine Kinases
		Three pharmacophore searching methods were applied to finding potential ATP-competitive inhibitors of the Tyrosine Kinase family: i) manual pharmacophore modeling (MOE), ii) “fuzzy” pharmacophore models (SQUID), and iii) similarity searching based on correlation-vector representations of potential pharmacophore-points (CATS3D).
	www.combichem.net (604 words)

	The Electronic Chemistry Library
		Searchable by material type, trade name, property parameters, manufacturer, etc.
		Free web site with Java-based (JME) interface for searching substructure, similarity and pharmacophore similarity on a collection of molecules.
		Also offers a chemical property calculation function for determining estimated logP (octanol-water partition coefficient), PSA, etc.
	www.lib.utexas.edu /chem/internet.html (4109 words)

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