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From owner-molmodel@hgmp.mrc.ac.uk  Wed Feb  6 02:33:54 2002
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> <option value=3D"NC">NC</option> <option value=3D"ND">ND</option> <option=
 value=3D"NE">NE</option> <option value=3D"NH">NH</option> <option value=3D=
"NJ">NJ</option> <option value=3D"NM">NM</option> <option value=3D"NV">NV</=
option> <option value=3D"NY">NY</option> <option value=3D"OH">OH</option> <=
option value=3D"OK">OK</option> <option value=3D"OR">OR</option> <option va=
lue=3D"PA">PA</option> <option value=3D"RI">RI</option> <option value=3D"SC=
">SC</option> <option value=3D"SD">SD</option> <option value=3D"TN">TN</opt=
ion> <option value=3D"TX">TX</option> <option value=3D"UT">UT</option> <opt=
ion value=3D"VA">VA</option> <option value=3D"VT">VT</option> <option value=
=3D"WA">WA</option> <option value=3D"WI">WI</option> <option value=3D"WV">W=
V</option> <option value=3D"WY">WY</option> </select><b> * <u>UNITED STATES=
 ONLY!</u></b></td></tr><tr> <td align=3D"RIGHT" width=3D"296" background=3D=
"Greenbackground=2Ejpg"> <font size=3D"2" color=3D"#000000" face=3D"Arial, =
Helvetica,sans-serif"><b> Zip/Postal Code</b></font></td><td width=3D"282">=
 <input type=3D"text" size=3D"10" maxlength=3D"15" name=3D"PostalCode"> *</=
td></tr><tr><td align=3D"RIGHT" width=3D"296" background=3D"Greenbackground=
=2Ejpg"> <font size=3D"2" color=3D"#000000" face=3D"Arial, Helvetica,sans-s=
erif"><b> Home Phone</b></font></td> <td width=3D"282"> <input type=3D"text=
" size=3D"20" maxlength=3D"30" name=3D"HPhone"> *</td></tr><tr> <td align=3D=
"RIGHT" width=3D"296" background=3D"Greenbackground=2Ejpg"> <font size=3D"2=
" color=3D"#000000" face=3D"Arial, Helvetica,sans-serif"><b> Work Phone</b>=
</font></td><td width=3D"282"> <input type=3D"text" size=3D"20" maxlength=3D=
"55" name=3D"WPhone"> *</td></tr><tr> <td align=3D"RIGHT" width=3D"296" bac=
kground=3D"Greenbackground=2Ejpg"> <font size=3D"2" color=3D"#000000" face=3D=
"Arial, Helvetica,sans-serif"><b> Email Address</b></font></td><td width=3D=
"282"> <input type=3D"text" size=3D"20" maxlength=3D"30" name=3D"Email"> *<=
/td></tr><tr> <td align=3D"RIGHT" width=3D"296" background=3D"Greenbackgrou=
nd=2Ejpg"> <font size=3D"2" color=3D"#000000" face=3D"Arial, Helvetica,sans=
-serif"><b> Best Time To Call</b></font></td><td width=3D"282" background=3D=
"Greenbackground=2Ejpg"> <select size=3D"1" name=3D"CallTime"> <option valu=
e=3D"Morning at Home" selected>Morning at Home</option> <option value=3D"Mo=
rning at Work">Morning at Work</option> <option value=3D"Afternoon at Home"=
>Afternoon at Home</option> <option value=3D"Afternoon at Work">Afternoon a=
t Work</option> <option value=3D"Evening at Home">Evening at Home</option> =
<option value=3D"Late Evening at Work">Late Evening at Home</option> </sele=
ct> *</td></tr><tr> <td align=3D"RIGHT" width=3D"296" background=3D"Greenba=
ckground=2Ejpg"> <font size=3D"2" color=3D"#000000" face=3D"Arial, Helvetic=
a,sans-serif"><b> Do You Own Your Home?</b></font></td><td width=3D"282" ba=
ckground=3D"Greenbackground=2Ejpg"> <select size=3D"1" name=3D"Homeowner"> =
<option value=3D"Yes" selected>Yes</option> <option value=3D"No">No</option=
> </select><font color=3D"#000000" size=3D"1"> * Mobile Homes Do Not Qualif=
y</font></td></tr><tr> <td align=3D"RIGHT" width=3D"296" background=3D"Gree=
nbackground=2Ejpg"> <font size=3D"2" color=3D"#000000" face=3D"Arial, Helve=
tica,sans-serif"><b> Property Value</b></font></td><td width=3D"282"> <inpu=
t type=3D"text" size=3D"13" name=3D"PropertyValue" onBlur=3D"if (!validate =
(this=2Evalue>=3D 50000)) { alert('Not Valid! Please enter the approximate =
value of current property or property you wish to purchase \n (greater than=
 or equal to 50000) using only number characters - 0123456789'); this=2Efoc=
us(); this=2Eselect(); return false; }"> * <font size=3D"1" color=3D"#00000=
0">Please use numbers only</font></td></tr><tr> <td align=3D"RIGHT" width=3D=
"296" background=3D"Greenbackground=2Ejpg"> <font color=3D"#000000" face=3D=
"Arial, Helvetica,sans-serif" size=3D"2"><b>Property Type</b></font></td> <=
td width=3D"282" background=3D"Greenbackground=2Ejpg"> <select size=3D"1" n=
ame=3D"PropertyType"> <option value=3D"Single Family Residence" selected>Si=
ngle Family Residence</option> <option value=3D"Condo">Condo</option> <opti=
on value=3D"Townhouse">Townhouse</option> <option value=3D"2-4 Plex">2-4 Pl=
ex</option> <option value=3D"Other">Other</option> </select> *</td></tr><tr=
> <td align=3D"RIGHT" width=3D"296" background=3D"Greenbackground=2Ejpg"> <=
font size=3D"2" color=3D"#000000" face=3D"Arial, Helvetica,sans-serif"><b> =
Purchase Price</b></font></td><td width=3D"282"> <input type=3D"text" size=3D=
"13" name=3D"PurchasePrice"> * <font size=3D"1" color=3D"#000000">Please us=
e numbers only</font></td></tr><tr> <td align=3D"right" width=3D"296" backg=
round=3D"Greenbackground=2Ejpg"> <font size=3D"2" color=3D"#000000" face=3D=
"Arial, Helvetica,sans-serif"><b><p> Year Acquired</b></font></td><td align=
=3D"left" width=3D"282"> <input type=3D"text" name=3D"YearAcquired" size=3D=
"13"> *</td></tr><tr align=3D"CENTER"> <td align=3D"RIGHT" width=3D"296" ba=
ckground=3D"Greenbackground=2Ejpg"> <font color=3D"#000000" face=3D"Arial, =
Helvetica,sans-serif" size=3D"2"><b>1st Mortgage-Balance Owed</b></font></t=
d> <td width=3D"282" align=3D"left"> <input type=3D"text" size=3D"13" maxle=
ngth=3D"30" name=3D"Mortgage1" onBlur=3D"if (!validate (this=2Evalue)) { al=
ert('Not Valid! Please enter only number characters - 0123456789\n If you h=
ave no current mortgage please enter 0'); this=2Efocus(); this=2Eselect(); =
return false; }"> * <font size=3D"1" color=3D"#000000">Please use numbers o=
nly (ex:45000) enter 0 for none</font></td></tr> <tr align=3D"center"> <td =
align=3D"RIGHT" width=3D"296" background=3D"Greenbackground=2Ejpg"> <font c=
olor=3D"#000000" face=3D"Arial, Helvetica,sans-serif" size=3D"2"><b>1st Mor=
tgage-Interest Rate</b></font></td> <td width=3D"282" align=3D"left"><b> <s=
elect size=3D"1" name=3D"CurrentIntRate"> <option value=3D"10=2E0" selected=
>10 or above</option> <option value=3D"7=2E0">Below 7=2E0</option> <option =
value=3D"7=2E25">7=2E1 - 7=2E49</option> <option value=3D"7=2E75">7=2E5 - 7=
=2E99</option><option value=3D"8=2E0">8=2E0 - 8=2E49</option> <option value=
=3D"8=2E75">8=2E5 - 8=2E99</option> <option value=3D"9=2E25">9=2E0 - 9=2E49=
</option> <option value=3D"9=2E75">9=2E5 - 9=2E99</option> <option value=3D=
"0">None</option> </select> %</b></td></tr><tr align=3D"center"><td align=3D=
"RIGHT" width=3D"296" background=3D"Greenbackground=2Ejpg"> <font size=3D"2=
" color=3D"#000000" face=3D"Arial, Helvetica,sans-serif"><b> Is 1st Adjusta=
ble or Fixed?</b></font></td><td align=3D"LEFT" width=3D"282" background=3D=
"Greenbackground=2Ejpg"> <select size=3D"1" name=3D"FirstType"> <option val=
ue=3D"Fixed" selected>Fixed</option> <option value=3D"Adjustable">Adjustabl=
e</option> </select> *</td></tr> <tr align=3D"center"> <td align=3D"RIGHT" =
width=3D"296" background=3D"Greenbackground=2Ejpg"> <font color=3D"#000000"=
 face=3D"Arial, Helvetica,sans-serif" size=3D"2"><b>Employer</b></font></td=
> <td width=3D"282" align=3D"left"> <input type=3D"text" size=3D"15" maxlen=
gth=3D"30" name=3D"Employer"> *</td></tr><tr align=3D"center"><td align=3D"=
RIGHT" width=3D"296" background=3D"Greenbackground=2Ejpg"> <font size=3D"2"=
 color=3D"#000000" face=3D"Arial, Helvetica,sans-serif"><b> Monthly Gross&n=
bsp;Household Income</b></font></td><td width=3D"282" align=3D"left"> <inpu=
t type=3D"text" size=3D"13" maxlength=3D"30" name=3D"MonthlyGrIncome"> * <f=
ont size=3D"1" color=3D"#000000">Please use numbers only</font></td></tr> <=
tr align=3D"center"> <td align=3D"RIGHT" width=3D"296" background=3D"Greenb=
ackground=2Ejpg"> <font size=3D"2" color=3D"#000000" face=3D"Arial, Helveti=
ca,sans-serif"><b> 2nd Mortgage Balance owed</b></font></td><td width=3D"28=
2" align=3D"left"> <input type=3D"text" size=3D"13" maxlength=3D"30" name=3D=
"Mortgage2" onBlur=3D"if (!validate (this=2Evalue)) { alert('Not Valid! Ple=
ase enter only number characters - 0123456789\n If you have no second mortg=
age please enter 0'); this=2Efocus(); this=2Eselect(); return false; }">> *=
 <font size=3D"1" color=3D"#000000">Please use numbers only(ex:45000) enter=
 0 for none</font></td></tr><tr align=3D"center"> <td align=3D"RIGHT" width=
=3D"296" background=3D"Greenbackground=2Ejpg"> <font color=3D"#000000" face=
=3D"Arial, Helvetica,sans-serif" size=3D"2"><b>Amount You Wish To Borrow</b=
></font></td> <td width=3D"282" align=3D"left"> <select size=3D"1" name=3D"=
BorrowRequest"> <option value=3D"25000" selected>15,000 - 30,000</option> <=
option value=3D"40000">30,000 - 45,000</option> <option value=3D"55000">45,=
000 - 60,000</option> <option value=3D"70000">60,000 - 75,000</option> <opt=
ion value=3D"85000">75,000 - 90,000</option> <option value=3D"105000">90,00=
0 - 110,000</option> <option value=3D"120000">110,000 - 125,000</option> <o=
ption value=3D"150000">125,000 &amp; Up</option> </select> *</td></tr><tr a=
lign=3D"center"> <td align=3D"RIGHT" width=3D"296" background=3D"Greenbackg=
round=2Ejpg"> <font size=3D"2" color=3D"#000000" face=3D"Arial, Helvetica,s=
ans-serif"><b> Credit Rating</b></font></td><td width=3D"282" align=3D"left=
"> <select size=3D"1" name=3D"CreditRating"> <option value=3D"Good" selecte=
d>Good</option> <option value=3D"Fair">Fair</option> <option value=3D"Poor"=
>Poor</option> <option value=3D"Excellent">Excellent</option> </select> *</=
td></tr><tr align=3D"center"> <td align=3D"RIGHT" width=3D"296" background=3D=
"Greenbackground=2Ejpg"> <font size=3D"2" color=3D"#000000" face=3D"Arial, =
Helvetica,sans-serif"><b> Monthly Debt</b></font></td><td width=3D"282" ali=
gn=3D"left"> <input type=3D"text" size=3D"13" name=3D"MonthlyDebt"> * <font=
 color=3D"#000000" size=3D"1">Please use numbers <b>only</b></font></td></t=
r><tr valign=3D"middle"> <td align=3D"RIGHT" width=3D"296" background=3D"Gr=
eenbackground=2Ejpg"> <font size=3D"2" color=3D"#000000" face=3D"Arial, Hel=
vetica,sans-serif"><b> Loan Interested In</b></font></td><td width=3D"282" =
align=3D"left"> <select size=3D"1" name=3D"LoanInterested"> <option value=3D=
"Debt Consolidation" selected>Debt Consolidation</option> <option value=3D"=
Second Mortgage">Second Mortgage</option> <option value=3D"Home Improvement=
">Home Improvement</option> <option value=3D"Refinance">Refinance</option> =
<option value=3D"Purchase">Purchase</option> </select> *<br>&nbsp;</td></tr=
><tr align=3D"center"> <td align=3D"center" colspan=3D"2" width=3D"582" "><=
p><b><font face=3D"Arial">Fast &amp; Easy -You Are Done !</font></b><br> <i=
nput type=3D"submit" value=3D"Submit This Application"></td></tr></table></=
td></tr></table> </form><p><font face=3D"Helvetica, sans-serif, Arial" size=
=3D"2">REMOVAL INSTRUCTIONS: This message is being sent to you in complianc=
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mmediate removal you may simply use reply on your email program with &quot;=
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begin 666 Incredable Gain.txt
M#0H-"@T*22=L;"!M86ME('EO=2!A('!R;VUI<V4N(%)%040@5$A)4R!%+4U!
M24P@5$\@5$A%($5.1"$@+2!F;VQL;W<@=VAA="!I="!S87ES('1O('1H92!L
M971T97(@+2!A;F0@>6]U('=I;&P@;F]T('=O<G)Y('=H971H97(@82!214-%
M4U-)3TX@:7,@8V]M:6YG(&]R(&YO="P@=VAO(&ES(%!R97-I9&5N="P@;W(@
M=VAE=&AE<B!Y;W4@:V5E<"!Y;W5R(&-U<G)E;G0@:F]B(&]R(&YO="X@665S
M+"!)(&MN;W<@=VAA="!Y;W4@87)E('1H:6YK:6YG+B!)(&YE=F5R(')E<W!O
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M:&%D('1O('=A:70@=6YT:6P@22!W87,@92UM86EL960@86=A:6X@8GD@<V]M
M96]N92!E;'-E+BXN+BXN+BXN,3$@;6]N=&AS('!A<W-E9"!T:&5N(&ET(&QU
M8VMI;'D@8V%M92!A9V%I;BXN+BXN+B!)(&1I9"!N;W0@9&5L971E('1H:7,@
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M;6%D92 D-38P+C P(&%N9"!B>2!T:&4@96YD(&]F('1H:7)D(&UO;G1H(&UY
M('1O=&%L(&-A<V@@8V]U;G0@=V%S("0S-C(L.#0P+C P+B!,:69E(&ES(&)E
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M/3T]/3T]/3T]/3T]/3T]/3T]/3T]/3T]/3T]/3T]#0H-"D]21$52(%E/55(@
M4D503U)44R!43T1!62!!3D0@1T54(%-405)4140@3TX@64]54B!23T%$(%1/
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M:&EN9W1O;BP@5FER9VEN:6$@;W(@0V%L:69O<FYI82P@<V-R965N:6YG(&]F
M(&%D9')E<W-E<R!H87,@8F5E;B!D;VYE('1O('1H92!B97-T(&]F(&]U<B!T
M96-H;FEC86P@86)I;&ET>2X-"@T**B @5&AI<R!I<R!A(&]N92!T:6UE(&UA
M:6QI;F<@86YD('1H:7,@;&ES="!W:6QL(&YE=F5R(&)E('5S960@86=A:6XN
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!"@``
`
end


From owner-molmodel@hgmp.mrc.ac.uk  Sun Feb 17 18:34:30 2002
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From: jianquan@eden.rutgers.edu (jianquan)
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Subject: The perspective of molecular docking:A killer application to drug design is emerging
Date: 17 Feb 2002 10:20:27 -0800
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The perspective of molecular docking: 
A killer application to drug design is emerging

by Jianquan Chen 
Email: chen_jianquan@yahoo.com

As structural genomics initiative begins to bring more and more 3D  
macromolecular structures, the work involved to validate all these 
potential targets, to demonstrate their therapeutic relevance, and to 
find
leads will become heavily dependent on the high-throughput screening 
technologies such as automated molecular docking.

Now it makes more and more chemical compounds screened because a new 
drug 
has to meet more and stricter requirements. Thus high-throughput
screening (HTS) technology has played an increasingly important role in 
new
drug development. And for many pharmaceutical companies, HTS is now an 
essential component to identify leads.

Molecular docking over a large scale virtual compound database is a 
kind of
virtual HTS technology. Molecular docking is used to predict the bound 
conformation of the ligand to the receptor. It connects the structural 
bioinformatics and drug design. Straightforwardly speaking, it is a 
tool 
to mine gold from the structural bioinformatics data. It can be divided 
into
3 classes, rigid ligand/rigid receptor, flexible ligand/rigid receptor, 
flexible ligand/(partially) flexible receptor docking. Rigid 
ligand/rigid 
receptor docking is very fast but not detailed. flexible ligand/ 
(partially)
flexible receptor docking is too complicated to be used to screen a 
large 
scale database. So we only discuss flexible ligand/rigid receptor 
docking. 

A docking problem can be divided into search algorithm and scoring 
function. 
search algorithm should be efficient enough to find the lowest energy 
configuration or conformation. The scoring function should be able to 
distinguish a correct binding mode from other putative modes. I only 
discuss search algorithm here because the progress on the search 
algorithm
and the computer will remove the hardware obstacle for the flexible 
ligand/
rigid receptor docking to enter the medicinal chemistry lab soon.

AEDock1.1, a new release of AEDock, where a new technology is 
introduced, 
can dock XK263, a bulky ligand with 10 rotatable bonds, into HIV-1 
protease 
in 23.4 seconds using a tolerance of 0.01nm rmsd with a success rate of 
92% 
on a PC with an AMD 750M CPU+256M SDRAM. Please read the results of 
AEDock1.1 at 
http://www20.brinkster.com/jianquan/aedock11/default.asp .It is a WHOLE 
MOLECULE-BASED docking program and so avoids the disadvantages of the 
fragment-based docking approaches. Based on the rotatable bond 
distribution 
table from Bohdan W., it is estimated that 2 PC with 2.2GHz Intel CPU 
can 
screen 1M drug-like compounds with 0-10 rotatable bonds in 1 week. 
Please 
follow the above link to see how it is estimated.

Comparison of molecular docking and real HTS 
1.Molecular docking over a compound database is more productive and 
cost-efficient than a real HTS. 
I list the disadvantages of real HTS here:
1. HTS is no guarantee of success.
2. Establishing a robust assay for a new target takes time and money. 
Hit rates against some receptors are reported to be very low, 
necessitating 
screening of very large numbers of com-pounds (tens to hundreds of 
thousands).
Collections of synthesized compounds or natural products often contain 
far 
less chemical diversity than is desired, are not bottomless resources, 
and 
are very time-consuming to replenish.
3. Techniques such as combinatorial chemistry offer the potential for 
synthesizing very large libraries of compounds, but in practice this 
approach
is time-consuming for drug-like com-pounds and may still produce 
libraries 
of relatively restricted diversity.
4. What is the most important is that a real HTS system and a real 
compound database are so expensive that only companies can afford them.
A normal medicinal chemistry lab can't afford it.

Bohdan W. etc. used a 64-processor SGI Origin2000 to dock a 1.1 million 
drug-like compounds and it took the workstation 6 days to finish the 
job. 
These compounds were docked into human alpha-estrogen receptor. after 
being docked and filtered by some supplementary descriptors, a set 
comprising
37 commercially available compounds were chosen to be assayed in a 
standard 
competitive radio-ligand binding assay. 21 exhibited an inhibition 
constant 
( Ki ) of 300 nM (nanomolar) or less, with the best compounds at 8 nM. 
Given 
the structural novelty of the hits (compounds known to possess 
estrogenic 
activity or to be structurally similar to known ligands were excluded 
from 
assay), this represents a very positive result, demonstrating that 
virtual 
screening can readily identify potent ligands from a variety of 
structural 
classes. 

Maybe you will say:"a 64-processor SGI Origin2000 is very expensive." 
But 
if AEDock1.1 is used, then we only need to buy 2 PC 2.2GHz Intel CPU. A 
Dell Dimension 8200 PC with 2.2G Pentium 4 CPU and 256MB PC800 RDRAM 
(Rambus dynamic RAM) only costs you $1,689 in Feb 13,2002. The total 
is about $3,300. Several months later they can be bought at a cheaper 
price. I predict in the end of 2002 a PC with one single CPU can screen 
1M drug-like compounds with 0-10 rotatable bonds using whole molecule-
based 
flexible ligand/rigid receptor docking approach in 1 week because 
performances of CPU and search algorithm are keeping increasing. It 
means
that the hardware obstacle for the flexible docking/rigid receptor 
docking
to enter normal medicinal chemistry lab will disappear soon.

Comparison of molecular docking and pharmacophore queries or focused 2-
D 
property
the flexible ligand/rigid docking is more detailed and more objective 
than pharmacophore queries or focused 2-D property. Application of 
pharmacophore queries or focused 2-D property profiles may significantly
inhibit the diversity of the compound subset because they are biased 
by the properties of known ligands. In contrast, the molecular docking
program can process an entire chemical database with minimal 
pre-filtering (e.g., to eliminate unstable or toxic moieties) so that 
the final selection is based on the quality of the docked models rather 
than a subjective opinion of what properties are expected in a ligand. 
This route is a very promising one to find structurally novel ligands, 
which may make receptor interactions similar to known ligands.
The roles molecular docking plays in the drug design
1. find leads.
2. provide groups for chemists to modify the leads. When compounds are 
docked into the receptor,  the groups interacting with the subsites of 
the receptor should be ranked. Maybe the groups with good ranking plus 
leading compounds will lead to final products. (up to now I didn't find 
any paper on this role of the molecular docking, please tell me if you 
find any paper on this. )

So molecular docking provides not only leading compounds, but also 
suggest
you how to modify the leads. Oops, molecular docking provides a whole 
solution for drug discovery.

It sounds molecular docking very promising and will be popular soon.
Then why not to invest your money or energy in it? Please contact me 
if you are interested. Email:chen_jianquan@yahoo.com, Phone:(USA)732-
207-8147

In a word, the molecular docking will become a killer application to 
drug 
design. It will enter the normal medicinal chemistry labs, not only the 
big pharmaceutical companies.

The obstacles for the molecular docking to enter the medicinal 
chemistry lab
1. The virtual compound database. Now most of the scientist uses ACD-3D 
or ACD-SC from MDL as the compound database for screening. It will cost 
you about $15,000 to get a license of ACD-3D and ACD-SC on a single 
"Datastation" per year. But MDL allows you to share the ISIS databases 
with other scientists and so it will lower your cost. In addition you 
need a license of Enterprise Oracle database. It seems the database 
costs 
you lots of money. There is an alternative solution. A free NCI 3D 
compound 
database can be stored in free database such as Mysql. After being 
screened 
the final set of compound can be submitted to www.chemexper.com to know 
if 
the compound is commercially available. In addition Oracle database is 
too 
difficult for a chemist or molecular modeler to maintain. 

2. The available 3D macromolecular structures. Most of the 3D 
structures 
of macromolecules are not available.  Fortunately, structural genomics 
initiative begins to bring more and more 3D macromolecular structures 
and 
maybe computational protein folding will bring some reliable structures.

3. The scoring functions and the accuracy of the 3D macromolecular 
structures.
Not all crystallographic structures can be reproduced because the 
scoring 
function can't distinguish a correct binding mode from other putative 
modes 
for some cases or some crystallographic structures are not accurate 
enough. 
Please tell me that if you find any paper on test a scoring functions using 
hundreds 
of PDB entries.

Please sent comments to chen_jianquan@yahoo.com or visit 
http://www20.brinkster.com/jianquan/aedock11/default.asp or my homepage
(http://www-ec.njit.edu/~jc26/). 

Note:(1) some contents are extracted from 
"Large-scale virtual screening for discovering leads in the postgenomic 
era", 
Waszkowycz, B.; Perkins, T. D. J.; Sykes, R. A.; Li, J. . IBM SYSTEMS 
J., 
2001, 40, 360-376.

(2) please include the web address of this paper 
(http://www20.brinkster.com/jianquan/aedock11/perspective.asp) 
and my name if you want to cite the opinions in this paper.


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Subject: Seqs, synths, mass specs, MALDIs, NMRs available
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Sequencers, synthesizers, Mass Specs, MALDIs, NMRs available:

Oligosynthesizers:
  Expedite 8909: $15,500. Trityl monitoring; rebuilt; 90-day warranty.
M.O.S.S. avail.
  BLP 192: New instrument. $120,000; 2 96-well plates; 8 min. cycle time.
  ABI 394: $12,500. Rebuilt; 90-day warranty
  ABI 3948: $20,000 obo. Working well in lab now.
  Beckman 1000M: $11,000; guaranteed working.
  ALF Express: $10,000. 1996 model; recently PM'd
  BioSearch 8750 ~$4,000. Have 5; cheaper & faster than 394s
  Cruachem PS250 <=$2,500. 6 available

Oligosequencers:
  ABI 3700: $165,000; includes AB install.
  MegaBace 1000: $65,000. Amersham install included
  ABI 377: $19,500. 64-lane; price includes ABI install
  ABI 377: $24,000. 96-lane; Sequencing mod.; under svc. contract; includes
ABI install
  ABI 373: $9,000. Stretch, Big Dye.
  ABI 373: $7,000. Non-stretch, Big Dye.
  ABI Genescan v. 3.1 software: $5,000. Legal copy; works on 310, 373 and
377.
  Li-Cor 4200: $39,000; factory certified; includes global upgrade.
  Li-Cor 4000LS <$20,000. 1994 model

Peptide synthesizers:
  ABI 430: $10,500. Rebuilt, 90-day warranty
  ABI 431: $19,000. Rebuilt, 90-day warranty
  ABI 432: $15,000. Rebuilt, 90-day warranty
  ABI 433: $34,000. Rebuilt, 90-day warranty
  ACT LabTech III: $15,000; 30-day warranty
  PerSeptive 9050+: $11,000. Rebuilt, 90-day warranty
  PerSeptive 9600: $6,000 Working in lab
  Rainin Sonata: $29,700. Refurbed/warranteed/installed
  PerSeptive Pioneer: $55,000 W/ MPS option (16 simultaneous). 1.5 yrs. old.
  ACT 200: $6,500. Used twice.
  ACT 400, 357-MPS: call for price. Very low use.

Peptide sequencers:
  Procise 492HT: $70,000, incl. AB install. AB service contract avail.
  Procise 491, 494HTs available; call for prices
  ABI 477/120 <=$5,000

[Note: various other ABI, HP, Millipore, Biosearch, Beckman, etc.
sequencers, synthesizers etc. available; please inquire.]

LC/MS & MS/MS:
  Sciex API 3000: $175,000. Mac; price incl. install and warr. + $12K/NT
upgrade.
  Sciex API 365: $60,000(!). current NT software; guaranteed good working
order.
  10x sensitivity upgrade for the 365: $75,000 installed.
   Sciex API 365: $125,000. With 10x sensitivity upgrade; performs like
current top-of-line instruments. Includes install/90-day warr.
  API 150: $49,000. Includes E. Coast install.
  Sciex API III+: $30,000. Triple quad: ES, APCI; +$15K/intall w/ 90-day
warr.
  API I: $20,000. single quad; more sensitive than the 150. +$15K/install &
1 yr. svc.
  Micromass Platform: call for price. 2 yrs. old; Waters 2690 hplc included
  Finnigan LCQ Classic: $75,000. Incl. ES, APCI, 4000 amu, install, 30-day
warr.
  Finnigan Navigator: $42,500. Guaranteed good working order.
  Finnigan TSQ 7000: $74,000. API 1; ES, APCI. +$5,000/install.
  Finnigan SSQ 7000: $40,000. ES, APCI; Excalibur, API 1; install incl.
  Finnigan MAT 95: $260,000. Hi res mag sector. 1994, ES, APCI, FAB,
Thermospray, GC interface, install, delivery, 1 yr warr.
  Finnigan MAT 900: $75,000. Offers considered. EI, ES, APCI.
  Finnigan MAT 90: $15,000. Hi-resolution magnetic sector
  Kratos Concept: $7,500 + price of removal
  VG70E-HF: $20,000 Hi-res mag sector; EI/CI, FAB. Recent refurb.
  Xtrell 400 ELQ: make offer. LC/MS/MS, GC/MS/MS; 10 yrs. old, floor model,
well-maintained
  Fisons VG 2000: <$100,000
  Fisons VG Trio: $25,000. LC + GC: 3000 amu; thermospray, EI/CI, HP 5890
   included. Install, license & 90-day warr. +: $14,500
  HP 5989: $21,500. Electrospray; APCI, 2000 amu.
  Nermag R10 10c: <$10,000. Like new; make offer

  Service and service contracts available for PESciex API 3000, 365 and
III+.

MALDI-TOFs:
  MicroMass Q-Tof 1: $170,000.
  Bruker Biflex III: ~$50,000. DE; decommissioned by Bruker.
  Voyager DE RP: $75,000. 4 yrs. old; price includes installation.
  Voyager LBT-2: $20,000. ~1993. Excellent condition. Non-DE.
  PerSeptive LaserTec II: $75,000. 5 yrs old; excellent condition.
  SRI custom design: $100,000 asking price. 384 samples/20 min. Can be
tested.
  Thermo/Finnigan Dynamo liner DE: $55,000, incl. ship, install, 90-day
warr.
  LaserMAT 2000: $24,000. New detector & laser; +$2,000/install; service
available
  VG Tof-Spec: $5,000. For parts: new laser card and other new boards.

GC/MS/MS:
  Finnigan GCQ: $35,000 4 yrs. old; well-maintained; install/svc contract
avail.

NMRs:
  Bruker AMX 500: $250,000. Installation included
  Varian ANOVA 400: $185,000. Broadband. Incl. install, 90-day warr.
  Varian Unity 500: $165,000. BB and C-P probes; pulsed field gradients; new
Sun wkstn; price includes install & warranty
  Varian Unity 300: $85,000. Incl. install, 90-day warranty.
  Bruker DMX 400: ~$150,000.
  Bruker Avance 400: $149,000. 1996; widebore. Includes install, 90-day
warr.
  Bruker AM 500: $125,000. Includes installation.
  Bruker AC 300: $69,000. Incl. install, 2 yr. warranty.
  Bruker AC 270: $58,000. Incl. install, 2 yr. warranty.
  Bruker AC 250: $58,000. Incl. install, 2 yr. warranty.
  Bruker QE 300: $79,000. TecMag Libra Power Mac. Incl. install.
  JEOL 270: $69,000. TecMag Libra Power Mac; includes install but not ship
  JEOL FX90q: $39,000. Installed w/ 90-day warr.
  Varian EM360: $16,500. Incl. install w/ 90-day warr.
  Bruker NR80: $19,000. Non-cryo; inexpensive; install available.
  Bruker NR80: $19,000. Non-cryo; price includes install but not shipping.

Liquid handlers:
  Packard Multiprobe Iiex: $30,000.
  Biomek 2000: offers considered.
  LC Packings UltiMate w/ FAMOS, used 4 mos., 20% discount from new price.

Other expensive hi-tech items:
  Axon Instrument GenPix 4000b laser scanner: $35,000. Like new.
  Affymetrix GeneArray Scanner, ~$68,000; Genechip Station, ~$25,000.
  Applied Biosystems 6700 Nucleic Acid Workstation: call for price.
  Genomic Solutions GeneTAC microarray Hybridization station: <= $45,000.
  BioRobotics BioPic automatic colony picker: $60,000; excellent condition.
  Various SEMs and TEMs, $9,500-$375,000. Call or email for list.

Too hard to classify:
  MD Phosphorimager 445SI incl. personal densitometer, $19,000.
  MD Personal Densitometer SI: call for price.
  MD PhosphorImager Model 425E: make offer.
  MD Phosphorimager Model 475: $15,000. Guaranteed working to specs.
  MD FluorImager SI, 1995 model, $14,500
  MD FluorImager 575; asking $18,500
  MD Cytosensor, ~ 50% of new price
  PE 9600 thermocyclers:: $4,750 guaranteed working
  PE 480 thermocyclers: $3,000 guaranteed working; have several
  Hitachi Model H-600AB transmission electron microscope, <: $20,000

Also available:
  HPLCs, ICs, CEs, FPLCs: microbore to prep scale
  Beckman, Tecan, Hamilton robots/liquid handlers
  A variety of other lab instruments.

Please call or email with your request. Listed items are subject to prior
sale.

[If you do not wish to receive this email list in future, please return this
message with the word "Remove" in the subject line and accept my apologies
for the inconvenience.]

Michael Sherrell
Grizzly Analytical (USA)
707 887 2919/fax 707 887 9834
www.grizzlyanalytical.com


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From owner-molmodel@hgmp.mrc.ac.uk  Wed Feb 27 21:05:06 2002
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Mike,


  Thanks again for lunch it was great!


Best regards,

Steve

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