From owner-chemistry@ccl.net Wed Nov 6 06:23:01 2019 From: "Joseph Leonard jleonard42^_^gmail.com" To: CCL Subject: CCL: Empirical metric for bond polarity in protein/ligand complex Message-Id: <-53870-191106062113-24100-HRt02wi6rU1oYmJTjOJirw__server.ccl.net> X-Original-From: Joseph Leonard Content-Type: text/plain; charset="UTF-8" Date: Wed, 6 Nov 2019 06:20:55 -0500 MIME-Version: 1.0 Sent to CCL by: Joseph Leonard [jleonard42-x-gmail.com] Folks, I would appreciate any pointers to such metrics. I am interested in evaluating the polarity of individual bonds in a binding pocket, based on the local environment. This would let me partition the pocket atoms, suggesting the bonds that would be appropriate to break. This strikes me as a problem that people have thought about in the past, possibly for single structures, but I can't remember an example that I have read. Thanks in advance! Joe Leonard jleonard42_._gmail.com -- Give my best to those I care for. With friends a simple nod will do. I bow to those who've come and gone before me. A handshake to the past... it gets me through. -- Little Feat From owner-chemistry@ccl.net Wed Nov 6 08:33:01 2019 From: "Tymofii Nikolaienko tim_mail---ukr.net" To: CCL Subject: CCL: Empirical metric for bond polarity in protein/ligand complex Message-Id: <-53871-191106082418-9371-sXWv6zCFLUbBRLDabqUdVw^server.ccl.net> X-Original-From: Tymofii Nikolaienko Content-Language: uk Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=utf-8; format=flowed Date: Wed, 6 Nov 2019 15:23:21 +0200 MIME-Version: 1.0 Sent to CCL by: Tymofii Nikolaienko [tim_mail=ukr.net] I think it is worth clarifying what kind of input data the desired metrics are expected to use? Sould it be, say, electron density distribution from quantum chemical modelling, semiempirical, or graph-based metrics ? Regards, Tymofii 06.11.2019 13:20, Joseph Leonard jleonard42^_^gmail.com пише: > Sent to CCL by: Joseph Leonard [jleonard42-x-gmail.com] > Folks, I would appreciate any pointers to such metrics. I am > interested in evaluating the polarity of individual bonds in a binding > pocket, based on the local environment. This would let me partition > the pocket atoms, suggesting the bonds that would be appropriate to > break. > > This strikes me as a problem that people have thought about in the > past, possibly for single structures, but I can't remember an example > that I have read. > > Thanks in advance! > > Joe Leonard > jleonard42,gmail.com > -- > Give my best to those I care for. > With friends a simple nod will do. > I bow to those who've come and gone before me. > A handshake to the past... > it gets me through. > -- Little Feat> > > > From owner-chemistry@ccl.net Wed Nov 6 10:38:00 2019 From: "Joe Leonard jleonard42[a]gmail.com" To: CCL Subject: CCL: Empirical metric for bond polarity in protein/ligand complex Message-Id: <-53872-191106103507-21613-ub8ZRJS4zlK+L27sMx39rQ * server.ccl.net> X-Original-From: Joe Leonard Content-Type: multipart/alternative; boundary="Apple-Mail=_9F0C915E-7944-4275-82FF-55426140F919" Date: Wed, 6 Nov 2019 10:34:58 -0500 Mime-Version: 1.0 (Mac OS X Mail 11.5 \(3445.9.1\)) Sent to CCL by: Joe Leonard [jleonard42**gmail.com] --Apple-Mail=_9F0C915E-7944-4275-82FF-55426140F919 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Sorry, I guess =E2=80=9Cempirical=E2=80=9D was insufficiently clear. I = am looking for a metric that can work from the protein/ligand complex = geometry directly - no wavefunction-based data as that would take far = too long to calculate. Joe > On Nov 6, 2019, at 8:23 AM, Tymofii Nikolaienko tim_mail---ukr.net = wrote: >=20 >=20 > Sent to CCL by: Tymofii Nikolaienko [tim_mail=3Dukr.net] > I think it is worth clarifying what kind of input data the desired = metrics are expected to use? >=20 > Sould it be, say, electron density distribution from quantum chemical = modelling, semiempirical, or graph-based metrics ? >=20 >=20 > Regards, > Tymofii >=20 >=20 > 06.11.2019 13:20, Joseph Leonard jleonard42^_^gmail.com =D0=BF=D0=B8=D1=88= =D0=B5: >> Sent to CCL by: Joseph Leonard [jleonard42-x-gmail.com] >> Folks, I would appreciate any pointers to such metrics. I am >> interested in evaluating the polarity of individual bonds in a = binding >> pocket, based on the local environment. This would let me partition >> the pocket atoms, suggesting the bonds that would be appropriate to >> break. >>=20 >> This strikes me as a problem that people have thought about in the >> past, possibly for single structures, but I can't remember an example >> that I have read. >>=20 >> Thanks in advance! >>=20 >> Joe Leonard >> jleonard42,gmail.com >> -- >> Give my best to those I care for. >> With friends a simple nod will do. >> I bow to those who've come and gone before me. >> A handshake to the past... >> it gets me through. >> -- Little Feat> >>=20 >>=20 >>=20 >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please = change>=20>=20>=20=>=20>=20Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 =E2=80=94 Give my best to those I care for. With friends a simple nod will do. I bow to those who've come and gone before me. A handshake to the past... it gets me through. -- Little Feat --Apple-Mail=_9F0C915E-7944-4275-82FF-55426140F919 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=utf-8 Sorry, I guess =E2=80=9Cempirical=E2=80=9D was insufficiently = clear.  I am looking for a metric that can work from the = protein/ligand complex geometry directly - no wavefunction-based data as = that would take far too long to calculate.

Joe

On Nov = 6, 2019, at 8:23 AM, Tymofii Nikolaienko tim_mail---ukr.net <owner-chemistry-#-ccl.net> wrote:


Sent to CCL by: Tymofii Nikolaienko [tim_mail=3Dukr.net]
I think it = is worth clarifying what kind of input data the desired metrics are = expected to use?

Sould it be, say, electron = density distribution from quantum chemical modelling, semiempirical, or = graph-based metrics ?


Regards,
Tymofii

06.11.2019 13:20, Joseph Leonard jleonard42^_^gmail.com =D0=BF=D0=B8=D1=88=D0=B5= :
Sent to CCL by: = Joseph Leonard [jleonard42-x-gmail.com]
Folks, I would = appreciate any pointers to such metrics.  I am
interested in evaluating the polarity of individual bonds in = a binding
pocket, based on the local environment. =  This would let me partition
the pocket atoms, = suggesting the bonds that would be appropriate to
break.

This strikes me as a problem that people have = thought about in the
past, possibly for single structures, = but I can't remember an example
that I have read.

Thanks in advance!

Joe Leonard
jleonard42,gmail.com
--
Give my best to those I care for.
With friends = a simple nod will do.
I bow to those who've come and gone = before me.
A handshake to the past...
it = gets me through.
  -- Little Feat>






-=3D This is automatically = added to each message by the mailing script =3D-
To = recover the email address of the author of the message, please change
the strange characters on the top line to the -#- sign. You can = also
look up the X-Original-From: line in the mail = header.

E-mail to subscribers: CHEMISTRY-#-ccl.net or = use:
    http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST-#-ccl.net or use
=     http://www.ccl.net/cgi-bin/ccl/send_ccl_message

http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/announcements/conferences/<= br class=3D"">
Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml

If your mail bounces from CCL with 5.7.1 = error, check:
    http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/



=E2=80=94
Give = my best to those I care for.
With friends a simple nod = will do.
I bow to those who've come and gone before = me.
A handshake to the past...
it gets me = through.
  -- Little Feat
<= /div>
<= /div>

= --Apple-Mail=_9F0C915E-7944-4275-82FF-55426140F919-- From owner-chemistry@ccl.net Wed Nov 6 11:12:00 2019 From: "Atte =?iso-8859-1?Q?Sillanp=E4=E4?= asillanp]![csc.fi" To: CCL Subject: CCL: HPC-Europa3 research visit funds: next DL 20th November Message-Id: <-53873-191106071225-9534-kSW/mcs4eAw9CtI1FP0kvw|server.ccl.net> X-Original-From: Atte =?iso-8859-1?Q?Sillanp=E4=E4?= Content-Type: multipart/alternative; boundary="=_e35bc962-af69-40d2-8864-0925f9f9bb70" Date: Wed, 6 Nov 2019 14:12:18 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Atte =?iso-8859-1?Q?Sillanp=E4=E4?= [asillanp^-^csc.fi] --=_e35bc962-af69-40d2-8864-0925f9f9bb70 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable HPCE3 is an EU programme funding research visits to 9 European countries (D= E, ES, FI, GR, IR, IT, NL, UK, SE) if the project requires HPC resources. V= isitors need to be come from an EU or affiliated state.[1] HPCE3 covers rea= sonable travel and accommodation costs and the local HPC-center gives CPU t= ime for 3-13 week long research visits. Choose from hundreds of hosts group= s already listed, list your own group (invite a researcher), or suggest a n= ew one.=20 Research can be of any scientific discipline, but chemists have been the mo= st successful in the first two years (132/109 applied/accepted in chemistry= , 115/101 in physics, and 454/359 overall). Browse abstracts of completed v= isits: http://www.hpc-europa.eu/visitors=20 The visitors and hosts have been satisfied according to feedback while the = online application is easy to fill in and acceptance rate is high. If you w= ant to visit an existing collaborator, start new collaboration, or e.g. pro= be a post-doc location, grab the opportunity!=20 Apply and read more in: http://www.hpc-europa.eu/=20 Processing applications takes ~1.5 months, so in practice, the visit could = start in January 2020 at the earliest and needs to start by May 2020. If yo= u miss this call, the next is in Feb 2020 (four every year).=20 On behalf of HPC-Europa3,=20 Atte Sillanp=E4=E4=20 [1] There is limited quota for researchers also from elsewhere=20 --=_e35bc962-af69-40d2-8864-0925f9f9bb70 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
HPCE3 is an EU programme funding research vis= its to 9 European countries (DE, ES, FI, GR, IR, IT, NL, UK, SE) if the pro= ject requires HPC resources. Visitors need to be come from an EU or affilia= ted state.[1] HPCE3 covers reasonable travel and accommodation costs and th= e local HPC-center gives CPU time for 3-13 week long research visits. Choos= e from hundreds of hosts groups already listed, list your own group (invite= a researcher), or suggest a new one.

Research can be of any scienti= fic discipline, but chemists have been the most successful in the first two= years (132/109 applied/accepted in chemistry, 115/101 in physics, and 454/= 359 overall). Browse abstracts of completed visits: http://www.hpc-europa.e= u/visitors

The visitors and hosts have been satisfied according to f= eedback while the online application is easy to fill in and acceptance rate= is high. If you want to visit an existing collaborator, start new collabor= ation, or e.g. probe a post-doc location, grab the opportunity!

Appl= y and read more in: http://www.hpc-europa.eu/

Processing application= s takes ~1.5 months, so in practice, the visit could start in January 2020 = at the earliest and needs to start by May 2020. If you miss this call, the = next is in Feb 2020 (four every year).

On behalf of HPC-Europa3,
=
Atte Sillanp=E4=E4

[1] There is limited quota for researchers also from elsewhere
--=_e35bc962-af69-40d2-8864-0925f9f9bb70--