Landry and Gies in their recent review paper "Drugs and their mol= ecular targets: an updated overview." bring it nicely to the point:

http://www.ncb= i.nlm.nih.gov/pubmed/18251718

Various ligands for a single target

Most of the target types can be either stimulated or inhibited, dependin= g on the ligand chosen. This leads to opposite regulations of related cellu= lar functions. Terms used to characterize these different ligand types diff= er according to the biochemical nature of the targets.

Enzyme ligands most often lead to inhibition of enzyme activity, binding= to the active site with competition with the substrate (competitive inhibi= tors) or to allosteric sites (non-competitive inhibitors). Activation of an= enzyme is more difficult, unless giving or generating an excess of substra= te or co-substrate.

Membrane transporters and ion channel permeability can be increased or d= ecreased by direct binding of selected drugs termed 'openers' and 'inhibito= rs' (or blockers) respectively. However, such ligands are too often imprope= rly referred to as 'agonists' and 'antagonists'.

Receptors of mediators interact with a large diversity of ligand types. = Agonists mimic the effects of endogenous mediators. Some exceptions to this= concept are now known, some couples of mediators acting through the bindin= g to a single receptor with agonist or antagonist properties, respectively,= i.e. interleukin-1 and interleukin-1 receptor antagonist protein (IRAP), R= ANK-L and osteoprotegerin (OPG), melanocortin (MSH) and agouti-related prot= ein (AGRP). Full agonists elicit a maximal response of the organism, usuall= y similar to that of the mediator. Partial agonists elicit a partial respon= se of the organism, and prevent the binding of the mediator. Thus the relat= ed function of the organism is decreased. Neutral antagonists prevent the b= inding of the mediator and thus abolish downstream physiological responses = caused by the mediator. Inverse agonists, also termed 'negative antagonists= ', have been found among antagonists. Similar to neutral antagonists, they = prevent the binding of agonists, including mediators, but elicit a response= inverse to that of agonists. Such ligands decrease the constitutive activi= ty of receptors [6,7].=

Receptors of mediators including intrinsic ion channels o= r enzyme activity have ligands in their receptor part (agonists and antagon= ists) as well as in their ion channel (openers and inhibitors or blockers) = or enzyme part (inhibitors).

Hope this helps.

Cheers,

Mireille

On 6/4/08, M= ichael Xu michael.drug.design ~~ gmail.com= <owner-chemistry|ccl.net= > wrote:

H= i, all

Recent days, some experts gave a wonderful expl= anation of IC50, Ki, Kd, and deltaG.

I am confused about some words several years. C= an anyone give some discussion?

Inhibitor

Agonist

Antagonist

Inverse agonist.

Is the inhibitor used for Enzyme-substrate-inhi= bitor?

And the agonist/antagonist used for protein-lig= and?

Thanks in advance.

Mike.

------=_Part_282_16906866.1212653867539-- From owner-chemistry@ccl.net Sun Jun 8 01:52:00 2008 From: "Rajarshi Guha rguha!=!indiana.edu" To: CCL Subject: CCL: Code for clustering !! Message-Id: <-37115-080608011830-3148-61ExEcgEI6Yy2M6+alOZKA .. server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Sun, 8 Jun 2008 01:18:06 -0400 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Rajarshi Guha [rguha:_:indiana.edu] -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Jun 6, 2008, at 12:27 AM, Pradipta Bandyopadhyay pradipta_b-*- mail.jnu.ac.in wrote: > > Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta_b ~ mail.jnu.ac.in] > Dear All, > > I am looking for a fortran code (or 2 codes) for hierarchical > clustering and k-means clustering. I want to use it for > clustering molecules based on energy and/or geometrical parameters. > I would appreciate any pointer. R will do this (depending to some extent on the size of your dataset) - ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- Q: What is a dyslexic, agnostic, insomniac? A: Someone who lays awake at night wondering if there really is a dog! -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkhLa44ACgkQZqGSLFHnnoQG9gCg7Z2kt+QQyqQx9z5ybF+yWCZ2 dVoAoOSnNoAey2++BjTnTmd62qcRcqOH =m1Yu -----END PGP SIGNATURE----- From owner-chemistry@ccl.net Sun Jun 8 02:28:00 2008 From: "Eric Scerri scerri|chem.ucla.edu" To: CCL Subject: CCL: New Book on Philosophy of Chemistry to be published in 3 days Message-Id: <-37116-080606120320-21767-PSxqBoH1970LiaAhDeZ3Ng_-_server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-6-377454067 Date: Fri, 6 Jun 2008 06:52:51 -0700 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Eric Scerri [scerri. _ .chem.ucla.edu] --Apple-Mail-6-377454067 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed Please see http://www.icpress.co.uk/chemistry/p548.html -------------l COLLECTED PAPERS ON PHILOSOPHY OF CHEMISTRY IMPERIAL COLLEGE PRESS. Publication Date June 9th, 2008. by Eric R Scerri (University of California in Los Angeles, USA) This book represents a collection of papers from one of the founders =20 of the new Philosophy of Chemistry. It is only the second single-=20 author collection of papers on the Philosophy of Chemistry. The author is the editor-in-chief of Foundations of Chemistry, the =20 leading journal in the field. He has recently gained worldwide =20 success with his book on the periodic table of the elements titled =20 The Periodic Table: Its Story and Its Significance. This volume =20 provides an in-depth examination of his more philosophical and =20 historical work in this area and further afield. Contents: * Philosophy of Chemistry and the Question of Reduction: * British Journal for Philosophy of Science, 1993? * The Case for Philosophy of Chemistry * Prediction of the Nature of Hafnium from Chemistry, Bohr=92s =20 Theory and Quantum Theory * Has Chemistry Been at Least Approximately Reduced to Quantum =20 Mechanics? * The Ontological Reduction of Chemistry * The Periodic Table, Electronic Configurations and the Nature =20 of the Elements: * Has the Periodic Table Been Successfully Axiomatized? * The Periodic Table: The Ultimate Paper Tool in Chemistry * Naive Realism, Reduction and the =91Intermediate Position=92 * How Ab Inito is Ab Initio Quantum Chemistry? Foundations of =20 Chemistry * Some Aspects of the Metaphysics of Chemistry and the Nature of =20= the Elements * Realism and Anti-Realism, and Educational Issues in Philosophy =20= of Chemistry: * Constructivism, Relativism and Chemistry * The Recently Claimed Observation of Atomic Orbitals and Some =20 Related Philosophical Issues * Normative and Descriptive Philosophy of Science and the Role =20 of Chemistry --Apple-Mail-6-377454067 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=WINDOWS-1252

Please see

http://www.icpress.c= o.uk/chemistry/p548.html

-------------l

COLLECTED PAPERS ON = PHILOSOPHY OF CHEMISTRY =A0 =A0 =A0= =A0

IMPERIAL COLLEGE PRESS. =A0

Publication Date June 9th, 2008.

by Eric R = Scerri (University of California in Los Angeles, USA)

This book = represents a collection of papers from one of the founders of the new = Philosophy of Chemistry. It is only the second single-author collection = of papers on the Philosophy of Chemistry.

The = author is the editor-in-chief of Foundations of Chemistry, the leading = journal in the field. He has recently gained worldwide success with his = book on the periodic table of the elements titled The Periodic Table: = Its Story and Its Significance. This volume provides an in-depth = examination of his more philosophical and historical work in this area = and further afield.

Contents:

=A0 =A0 * Philosophy of Chemistry and the Question of = Reduction:

=A0 =A0 * British Journal = for Philosophy of Science, 1993?

=A0 =A0 * = The Case for Philosophy of Chemistry

=A0 =A0 * = Prediction of the Nature of Hafnium from Chemistry, Bohr=92s Theory and = Quantum Theory

=A0 =A0 * Has Chemistry Been = at Least Approximately Reduced to Quantum Mechanics?

=A0 =A0 * The Ontological Reduction of = Chemistry

=A0 =A0 * The Periodic = Table, Electronic Configurations and the Nature of the = Elements:

=A0 =A0 * Has the Periodic = Table Been Successfully Axiomatized?

=A0 =A0 * = The Periodic Table: The Ultimate Paper Tool in = Chemistry

=A0 =A0 * Naive Realism, = Reduction and the =91Intermediate Position=92

=A0 =A0 * How Ab Inito is Ab Initio Quantum Chemistry? = Foundations of Chemistry

=A0 =A0 * = Some Aspects of the Metaphysics of Chemistry and the Nature of the = Elements

=A0 =A0 * Realism and = Anti-Realism, and Educational Issues in Philosophy of = Chemistry:

=A0 =A0 * Constructivism, = Relativism and Chemistry

=A0 =A0 * = The Recently Claimed Observation of Atomic Orbitals and Some Related = Philosophical Issues

=A0 =A0 * = Normative and Descriptive Philosophy of Science and the Role of = Chemistry=A0