From owner-chemistry@ccl.net Mon Jan 28 08:16:00 2013 From: "Andrew Voronkov drugdesign/./yandex.ru" To: CCL Subject: CCL: docking programs, which account for T-shaped pi-pi interactions Message-Id: <-48137-130128043134-19453-yMrb+8NexAltLQVtnXpigA!=!server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=koi8-r Date: Mon, 28 Jan 2013 13:31:19 +0400 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign[A]yandex.ru] Dear CCL users, we have published a model with docked ligand. The X-ray, which was done after publication shows that it was wrong. As I understand the cause for error was that in ligand-protein interactions the T-shaped stacking between ligand's aromatic ring and aromatic ring of Phe plays an important role. Docking was performed by GoldSuite. I have analyzed different docking poses and none of them was correct. I am curious about docking programs or docking poses evaluation methods, which can account for this type of interactions. Basically those, which can accurately reproduce different types of interactions, including this type and different types of pi interactions. That is probably quite general problem for docking. But I am just curious if docking methods can accurately account for such interactions, or that should be some quantum, mechanics methods or maybe this program from Shroedinger group http://www.schrodinger.com/productpage/14/18/? Has anyone been working with this type of interactions? Best regards, Andrew -------- Завершение пересылаемого сообщения -------- From owner-chemistry@ccl.net Mon Jan 28 08:51:00 2013 From: "Manjunath Ningappa Wari sm5wari^^^gmail.com" To: CCL Subject: CCL:G: Facing difficulty in running g03 peogramm Message-Id: <-48138-130128060310-18804-EbxHTm/rcLqM/WLP9bKXwQ(-)server.ccl.net> X-Original-From: "Manjunath Ningappa Wari" Date: Mon, 28 Jan 2013 06:03:09 -0500 Sent to CCL by: "Manjunath Ningappa Wari" [sm5wari^^gmail.com] I am calculating dipole moment in ground state for coumarine molecules using g03 program. It is taking very long time to calculate, so plz suggest me how to run faster the g03 program. Thanking you Manjunath Wari Dept of Physics Karnatk University Dharwad. e-mail: sm5wari(!)gmail.com From owner-chemistry@ccl.net Mon Jan 28 09:26:00 2013 From: "Mark ta L. Munzarov marketa]![chemi.muni.cz" To: CCL Subject: CCL: Running EHC in C.A.C.A.O.: Problems with input Message-Id: <-48139-130128060630-18981-aatjBOzIlQH45tlR47atXw===server.ccl.net> X-Original-From: "Mark ta L. Munzarov " Date: Mon, 28 Jan 2013 06:06:29 -0500 Sent to CCL by: "Mark ta L. Munzarov " [marketa-$-chemi.muni.cz] Dear CCL members, I am trying to run an Extended Hueckel Calculation in the program C.A.C.A.O using dosbox under free bsd. I have the following input: TITL calculation of MOs for IrS complex with Ir_S bond 2.13 A ^M KEYW EL CM NC WF RO^M FV1 2.31 2.32 2.33 2.34 2.35 2.36 2.37 2.38 ORIG IR INTZM 2 S FV1 INTZM 3 Cl 1 2.37 2 93.4 INTZM 4 Cl 1 2.36 2 91.1 3 90.7 INTZM 5 Cl 1 2.36 2 93.2 3 -178.9 INTZM 6 Cl 1 2.37 2 93.6 3 -89.0 INTZM 7 N 1 2.14 2 178.4 3 108.9 INTZM 8 O 2 1.47 1 118.6 3 88.7 INTZM 9 C 2 1.78 1 111.7 3 -36.1 INTZM 10 C 2 1.78 1 111.8 3 -146.4 INTZM 11 C 7 1.35 1 130.4 2 -158.4 INTZM 12 C 7 1.33 1 124.4 2 17.9 INTZM 13 H 9 1.09 2 107.3 1 67.0 INTZM 14 H 9 1.09 2 106.8 1 -173.6 INTZM 15 H 9 1.09 2 109.0 1 -52.5 INTZM 16 H 10 1.09 2 106.7 1 172.9 INTZM 17 H 10 1.09 2 107.3 1 -67.7 INTZM 18 H 10 1.09 2 109.1 1 51.8 INTZM 19 H 12 1.08 7 124.3 1 3.0 INTZM 20 N 12 1.33 7 111.9 1 -176.6 INTZM 21 H 20 1.01 12 124.4 7 179.5 INTZM 22 C 11 1.38 7 110.6 1 176.4 INTZM 23 N 11 1.35 7 129.1 1 -3.9 INTZM 24 H 23 1.02 11 119.0 7 -5.5 INTZM 25 C 22 1.41 11 119.6 7 -179.8 INTZM 26 C 23 1.34 11 117.5 7 -179.9 INTZM 27 N 25 1.32 22 123.2 11 179.8 INTZM 28 N 25 1.35 22 117.1 11 -0.2 INTZM 29 H 26 1.08 23 116.0 11 179.3 INTZM 30 H 27 1.01 25 117.9 22 2.3 INTZM 31 H 27 1.01 25 117.9 22 177.7 END^M After I run EHT, I get the following error message: "Integer FORMAT can't read field starting at column 13 in this line: INTZM 2 S FV1 Stop - Program terminated. " Can anybody see what is wrong in the input? Thank you very much, Marketa Munzarova marketa|chemi.muni.cz Masaryk University, Brno, Czech Republic From owner-chemistry@ccl.net Mon Jan 28 10:01:00 2013 From: "Jan Kuras jan.kuras{=}chemistrycentral.com" To: CCL Subject: CCL: Call for Papers: ACS Fall Mtg 2013 Symposium in Semantic Technologies Message-Id: <-48140-130128061002-19209-9D/I3oFj3niYCMV93Z1Luw.:.server.ccl.net> X-Original-From: "Jan Kuras" Date: Mon, 28 Jan 2013 06:10:01 -0500 Sent to CCL by: "Jan Kuras" [jan.kuras..chemistrycentral.com] Call for Papers Joint CINF-CSA Trust Symposium: Semantic Technologies in Translational Medicine & Drug Discovery 246th ACS National Meeting, Indianapolis, Indiana September 8-12, 2013 CINF Division Dear colleagues We are inviting submission of abstracts for a joint ACS Division of Chemical Information (CINF) and CSA Trust Symposium on Semantic Technologies in Translational Medicine & Drug Discovery. The last few years have seen an explosion of public and proprietary healthcare and drug discovery data, and in parallel the emergence of powerful semantic, network and visualization technologies for integrating and mining these data. These novel datasets and technologies open up many possibilities for drug discovery and translational medicine, including drug repurposing, target identification, gene-disease association and patient population mapping. In parallel, major efforts are underway, such as the US NCATS at NIH, that support translational medicine and streamlined discovery of new medical therapies in the public sphere. This session will showcase some of the challenges in this area and the ongoing research into semantics, drug discovery and translational medicine. We encourage papers to be submitted in this scope, in particular the following areas: * Large scale integration of heterogenous drug discovery data using semantic technologies * Algorithms and methodologies that use semantic drug discovery and medical data * Semantic technologies in scientific publication, including Nanopublications * Efforts to use semantic technologies in the pharmaceutical industry Presentations will be 25-30 minutes, including time for questions. The deadline for submitting an abstract for consideration is March 18, 2013. Abstracts may be submitted via the ACS online Program & Abstract Creation System (PACS) at: http://abstracts.acs.org. You do not have to be an ACS member to create an account for PACS (although if you have a login for the ACS site, you can use that). Please do contact the co-organizers if you have any questions or to discuss a paper. Thank you, David Wild, Assistant Professor, Indiana University School of Informatics & Computing (djwild(a)indiana.edu) Jan Kuras, Publisher, Chemistry Central (jan.kuras(a)chemistrycentral.com) From owner-chemistry@ccl.net Mon Jan 28 10:36:00 2013 From: "Chris Swain swain]-[mac.com" To: CCL Subject: CCL: docking programs, which account for T-shaped pi-pi interactions Message-Id: <-48141-130128093141-9065-yde+LqUW4EARJUR++3r4yg:server.ccl.net> X-Original-From: Chris Swain Content-type: multipart/alternative; boundary="Boundary_(ID_KQ0HBy1tCnRvikhIHOjL5Q)" Date: Mon, 28 Jan 2013 14:31:32 +0000 MIME-version: 1.0 Sent to CCL by: Chris Swain [swain-*-mac.com] --Boundary_(ID_KQ0HBy1tCnRvikhIHOjL5Q) Content-type: text/plain; charset=utf-8 Content-transfer-encoding: quoted-printable Have you tried the Cresset software? http://www.cresset-group.com/ Chris Sent from my iPad On 28 Jan 2013, at 09:31, "Andrew Voronkov drugdesign/./yandex.ru" wrote: >=20 > Sent to CCL by: Andrew Voronkov [drugdesign[A]yandex.ru] > Dear CCL users, we have published a model with docked ligand. The X-ray, w= hich was done after publication shows that it was wrong. > As I understand the cause for error was that in ligand-protein interaction= s the T-shaped stacking between ligand's aromatic ring and aromatic ring of P= he plays an important role. Docking was performed by GoldSuite. > I have analyzed different docking poses and none of them was correct. > I am curious about docking programs or docking poses evaluation methods, w= hich can account for this type of interactions. > Basically those, which can accurately reproduce different types of interac= tions, including this type and different types of pi interactions. > That is probably quite general problem for docking. But I am just curious i= f docking methods can accurately account for such interactions, or that shou= ld be some quantum, mechanics methods or maybe this program from Shroedinger= group http://www.schrodinger.com/productpage/14/18/? Has anyone been workin= g with this type of interactions? >=20 > Best regards, > Andrew > -------- =D0=97=D0=B0=D0=B2=D0=B5=D1=80=D1=88=D0=B5=D0=BD=D0=B8=D0=B5 =D0=BF= =D0=B5=D1=80=D0=B5=D1=81=D1=8B=D0=BB=D0=B0=D0=B5=D0=BC=D0=BE=D0=B3=D0=BE =D1= =81=D0=BE=D0=BE=D0=B1=D1=89=D0=B5=D0=BD=D0=B8=D1=8F -------- >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script =3D= ->=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20>=20>=20>=20>=20 >=20 --Boundary_(ID_KQ0HBy1tCnRvikhIHOjL5Q) Content-type: text/html; charset=utf-8 Content-transfer-encoding: quoted-printable
Have you tried the Cresset software?


Chris

Sent f= rom my iPad

= On 28 Jan 2013, at 09:31, "Andrew Voronkov drugdesign/./yandex.ru" <owner= -chemistry(~)ccl.net> wrote:


Sent to C= CL by: Andrew Voronkov [drugdesign[A]yandex.ru<= /a>]
Dear CCL users, we have published a model with docked l= igand. The X-ray, which was done after publication shows that it was wrong.<= /span>
As I understand the cause for error was that in ligand-prote= in interactions the T-shaped stacking between ligand's aromatic ring and aro= matic ring of Phe plays an important role. Docking was performed by GoldSuit= e.
I have analyzed different docking poses and none of them w= as correct.
I am curious about docking programs or docking p= oses evaluation methods, which can account for this type of interactions.
Basically those, which can accurately reproduce different type= s of interactions, including this type and different types of pi interaction= s.
That is probably quite general problem for docking. But I= am just curious if docking methods can accurately account for such interact= ions, or that should be some quantum, mechanics methods or maybe this progra= m from Shroedinger group http://www.schrodinger.com/productpage/14/18/? Has anyone been w= orking with this type of interactions?

Best= regards,
Andrew
-------- =D0=97=D0=B0=D0=B2= =D0=B5=D1=80=D1=88=D0=B5=D0=BD=D0=B8=D0=B5 =D0=BF=D0=B5=D1=80=D0=B5=D1=81=D1= =8B=D0=BB=D0=B0=D0=B5=D0=BC=D0=BE=D0=B3=D0=BE =D1=81=D0=BE=D0=BE=D0=B1=D1=89= =D0=B5=D0=BD=D0=B8=D1=8F --------


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= = --Boundary_(ID_KQ0HBy1tCnRvikhIHOjL5Q)-- From owner-chemistry@ccl.net Mon Jan 28 11:43:01 2013 From: "John W Liebeschuetz john!^!ccdc.cam.ac.uk" To: CCL Subject: CCL: docking programs, which account for T-shaped pi-pi interactions Message-Id: <-48142-130128114019-8143-wWkWeZORACMkKWilqg8T0g%a%server.ccl.net> X-Original-From: "John W Liebeschuetz" Date: Mon, 28 Jan 2013 11:40:16 -0500 Sent to CCL by: "John W Liebeschuetz" [john,+,ccdc.cam.ac.uk] Dear Andrew, Whilst it is true that most docking scoring functions do not take account of T stacking pi-pi interactions as well as they do hydrogen bonding interactions, there may be another reason why your original docking did not give the experimental result. Have you investigated whether there is some movement of the protein in the more recent structure, that facilitates this T-stacking of aromatic groups? If so, including very accurate descriptions of T stacking in the docking algorithm may not be sufficient to get a good binding pose, when using your original protein model. Conversely a more general scoring function might reproduce the correct pose in the most recent protein model. Regards John Dr John W. Liebeschuetz Life Sciences Research & Applications Manager Cambridge Crystallographic Data Centre 12 Union Rd., Cambridge CB2 1EZ, UK From owner-chemistry@ccl.net Mon Jan 28 14:48:00 2013 From: "David L Mobley dmobley=uci.edu" To: CCL Subject: CCL: SAMPL4 binding/transfer challenge announcement Message-Id: <-48143-130128140415-31808-N3WZIqGVr1dGbTtPpoKNhw- -server.ccl.net> X-Original-From: "David L Mobley" Date: Mon, 28 Jan 2013 14:04:14 -0500 Sent to CCL by: "David L Mobley" [dmobley(!)uci.edu] Dear Colleagues, We are writing to invite your participation in the upcoming Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) 4 challenge. This challenge provides an opportunity for blind tests of computational methods for binding and hydration prediction as detailed below. Historically, a heavy focus of this meeting has been on free energy techniques for these applications, though other approaches are welcome as well. Our challenge this year includes protein-ligand binding, host-guest binding, and hydration free energy components. We expect to have representatives of a variety of major approaches and techniques participating, and would be delighted to have you or others in your group participate as well. Please pass this invitation along to anyone else who might be interested. To sign up for SAMPL4, please indicate your interest at http://sampl.eyesopen.com to indicate your interest (create an account to register and be notified as the data becomes available beginning in February; re-visit the site later to download the appropriate data and submit your predictions). A full description of the challenge is also available there, as well as at the end of this e-mail. Please contact us if you have any questions. Sincerely, David Mobley (UC Irvine) Tom Peat (CSIRO) Vijay Pande (Stanford) John Chodera (MSKCC) Michael Gilson (UC San Diego) Building on a series of successful blind challenges for computational chemistry, the SAMPL4 challenge will have hydration free energy, host-guest, and binding free prediction components. As with previous SAMPL challenges, the opportunity for blind predictions is available and the SAMPL project will culminate with a science meeting in September, 2013. In the host-guest prediction component, participants will be provided with the chemical structures of the host molecule and a set of guest molecules. In the present round, we will focus on two hosts. The first is CB7, which avoids the complexities encountered in SAMPL3 for a cucurbituril derivative with four carboxyl groups. The guests will be commercially available compounds expected to span a range of affinities. The experiments will yield relative binding affinities (via NMR and potentially supplemented by ITC), through competitive binding experiments, for the sake of experimental convenience. For a second host, we will focus on a basket-shaped octa-acid host studied by the Gibb lab, and experimental data will be similar (spanning 10 guests, all charged carboxylic acids), but with affinities measured by ITC. Protein-ligand binding prediction will focus on a set of HIV integrase inhibitors with affinities in the micromolar range. Nearly 400 compounds have been tested, and roughly 100 of these are known to bind with ~70 high-resolution crystal structures available. Challenge aspects will focus on three main categories for binding: (1) virtual screening, where participants attempt to identify the binders out of a small library of around 400 compounds; (2) binding mode/affinity prediction, where participants attempt to predict binding modes or binding modes and affinities; and (3) affinity prediction, where participants attempt to predict affinities (or relative affinities) given binding modes. Participation in challenge aspect (3) precludes participation in (1) or (2) unless the aspects are done sequentially. We are grateful to Avexa Ltd, Australia for the data. Hydration free energy prediction will focus on a dataset of around 500 small molecules with hydration free energies curated by J. Peter Guthrie, as in previous SAMPL challenges. Details on this aspect of the challenge are forthcoming. The challenge will begin soon with the hydration portion of the challenge and virtual screening of HIV integrase inhibitors. The host-guest challenge and the other components of the HIV integrase challenge will be available beginning in February as affinity data is finalized. The SAMPL4 meeting will take place September 20, 2013, at Stanford University. To give slightly more information on the data for the HIV integrase portion of the challenge, roughly 20 of the structures have already been published, so these compounds will be included in the challenge for purposes of completeness but will not be included in ranking of overall results, though participants may include these in their analysis. Compounds range from fragment-like to drug-size (~135 to 700 Da) and span a variety of chemistries. Binding affinity data is not necessarily available for all compounds, so tests #2 and #3 may focus on a smaller subset of compounds, though additional data is still being collected. Binding covers three different binding sites and affinities are often relatively weak, typically in the micromolar range. Crystal structures range from 1.65 to 2.15 angstrom resolution with good completeness and redundancy (98-100% complete, 5-fold redundancy in the data). From owner-chemistry@ccl.net Mon Jan 28 15:23:00 2013 From: "jessica koppen jvkoppen() oakland.edu" To: CCL Subject: CCL: NTOs and degenerate excited states Message-Id: <-48144-130128143140-421-46SE5f8Q5QZTUXYuIMsitw*server.ccl.net> X-Original-From: "jessica koppen" Date: Mon, 28 Jan 2013 14:31:39 -0500 Sent to CCL by: "jessica koppen" [jvkoppen{:}oakland.edu] I am running an NTO analysis on highly symmetric small gold clusters. I read the wonderful paper written by Richard Martin and understand that I need to find eigenvalues (lambda) close to 1. My question, if I have degenerate excited states which contribute to a particular bright state do I take the sum of the eigenvalues and verify that it is the sum that must be close to 1? For example, if I am looking at an E(g) state where 2 two transitions are contributing: Excited state 6 NTO output: 72 73 74 75 76 O O O O O Eigenvalues -- 0.02477 0.04323 0.04338 0.32176 0.54832 Excited state 7 NTO output: 72 73 74 75 76 O O O O O Eigenvalues -- 0.02487 0.04310 0.04339 0.32142 0.54856 do I take the sum of NTO76 for n=6 and n=7 --> 0.54832 + 0.54832 = 1.09712? This would confirm that NTO76 is my major contributor to this transition. If this is not correct than my eigenvalue of 0.54832 is no where near 1 and the NTO analysis will not work for these highly symmetric clusters. I would appreciate any insights. Thank you, Jessica Koppen From owner-chemistry@ccl.net Mon Jan 28 15:58:00 2013 From: "jessica koppen jvkoppen+*+oakland.edu" To: CCL Subject: CCL: NTOs and degenerate excited states Message-Id: <-48145-130128143821-656-kecOJ/JMXe/AH/MruxudiA\a/server.ccl.net> X-Original-From: "jessica koppen" Date: Mon, 28 Jan 2013 14:38:20 -0500 Sent to CCL by: "jessica koppen" [jvkoppen*_*oakland.edu] I am running an NTO analysis on highly symmetric small gold clusters. I read the wonderful paper written by Richard Martin and understand that I need to find eigenvalues (lambda) close to 1. My question, if I have degenerate excited states which contribute to a particular bright state do I take the sum of the eigenvalues and verify that it is the sum that must be close to 1? For example, if I am looking at an E(g) state where two transitions are contributing: Excited state 6 NTO output: 72 73 74 75 76 O O O O O Eigenvalues -- 0.02477 0.04323 0.04338 0.32176 0.54832 Excited state 7 NTO output: 72 73 74 75 76 O O O O O Eigenvalues -- 0.02487 0.04310 0.04339 0.32142 0.54856 do I take the sum of NTO76 for n=6 and n=7 --> 0.54832 + 0.54832 = 1.09712? This would confirm that NTO76 is my major contributor to this transition. If this is not correct than my eigenvalue of 0.54832 is no where near 1 and the NTO analysis will not work for these highly symmetric clusters. I would appreciate any insights. Thank you, Jessica Koppen