The June issue of=C2=A0Computati= onal Chemistry Highlights=C2=A0is out.

CCH is an=C2=A0overlay journal=C2=A0that identif= ies the most important papers in computational and theoretical chemistry pu= blished in the last 1-2 years. CCH is not affiliated with any publisher: it= is a free resource run by scientists for scientists.=C2=A0You can read more about it here.

Table of content for t= his issue features contributions from Steven Bachrach and Jan Jensen:

Triplet-Tuning: A Novel Non-Empirical Construction Scheme of Ex= change Functionals

Intramolecular London = Dispersion Interaction =C2=A0Effects on Gas-Phase and Solid-State Structure= s of Diamondoid Dimers

Interested in contributing? =C2=A0Read more her= e

Inter= ested in more?=C2=A0There are many ways to subscribe to CCH updates.

--0000000000006936c9057029c55c-- From owner-chemistry@ccl.net Wed Jul 4 09:52:00 2018 From: "HOUSTON Douglas DouglasR.Houston|ed.ac.uk" To: CCL Subject: CCL: Pharmacophore search tool Message-Id: <-53369-180704065139-19462-rFdwrv37CCmUMecNbYd9AQ]![server.ccl.net> X-Original-From: HOUSTON Douglas Content-Language: en-GB Content-Transfer-Encoding: binary Content-Type: multipart/mixed; boundary="----------=_1530701490-4310-7" Date: Wed, 4 Jul 2018 10:51:26 +0000 MIME-Version: 1.0 Sent to CCL by: HOUSTON Douglas [DouglasR.Houston*|*ed.ac.uk] This is a multi-part message in MIME format... ------------=_1530701490-4310-7 Received: from hbdat3.is.ed.ac.uk (129.215.235.38) by hbdat3.is.ed.ac.uk (129.215.235.38) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_128_GCM_SHA256) id 15.1.1466.3; Wed, 4 Jul 2018 11:51:28 +0100 Received: from EUR04-HE1-obe.outbound.protection.outlook.com (23.103.133.179) by hbdat3.is.ed.ac.uk (129.215.235.38) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_128_CBC_SHA256) id 15.1.1466.3 via Frontend Transport; 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x-forefront-prvs: 0723A02764 x-forefront-antispam-report: SFV:NSPM;SFS:(10009020)(366004)(396003)(39860400002)(376002)(346002)(136003)(189003)(199004)(54896002)(5660300001)(6606003)(33656002)(7116003)(8676002)(81156014)(2906002)(81166006)(7736002)(8936002)(74316002)(6436002)(6916009)(413944005)(72206003)(105586002)(55016002)(106356001)(25786009)(9686003)(478600001)(19627405001)(97736004)(74482002)(66066001)(476003)(486006)(11346002)(3846002)(6116002)(6506007)(316002)(99286004)(53936002)(2900100001)(86362001)(68736007)(786003)(446003)(256004)(5250100002)(76176011)(3480700004)(26005)(14454004)(186003)(102836004)(7696005);DIR:OUT;SFP:1101;SCL:1;SRVR:DB7PR05MB4938;H:DB7PR05MB4172.eurprd05.prod.outlook.com;FPR:;SPF:None;LANG:en;PTR:InfoNoRecords;MX:1;A:1; received-spf: None (protection.outlook.com: ed.ac.uk does not designate permitted sender hosts) x-microsoft-antispam-message-info: /n2tg3x1c3AOpGhQPmnogteMbjlQsMcohBOdNt5nDvINDSZMqSwzPFr622l8Rl1ki2E51X81dZhdGqf+RNYlOFewFdScvV1jitFbaspwG7uTJ/XUFxYFvoXBCfgtPGrvnKODKW2BKGNZ4PAlvkuKY0rMYLxRXACd6bX3bBHoUynOFrdU1DAgjEUL6mEpU5kLRG+Zmpi2dx8DE1rxNQtpVTHai1zn15XcicGi4rqixQLikzArcLzYi/iqVy/7koUW89WmSM69Ii+7Au1ESuhFr39WcRPTZOZocwCnqF7tBOUjEHEUi87ELUzhWZk808iVxqryRQiyGryiLdMdj72rFFfqfeM1vgq//qRAct5C2yk= spamdiagnosticoutput: 1:99 spamdiagnosticmetadata: NSPM Content-Type: multipart/alternative; boundary="_000_DB7PR05MB4172AC1975DD69E2607C1AE7A8410DB7PR05MB4172eurp_" MIME-Version: 1.0 X-MS-Exchange-CrossTenant-Network-Message-Id: 7a09c876-4b2b-4d0f-6cf8-08d5e19c1794 X-MS-Exchange-CrossTenant-originalarrivaltime: 04 Jul 2018 10:51:26.8063 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 2e9f06b0-1669-4589-8789-10a06934dc61 X-MS-Exchange-Transport-CrossTenantHeadersStamped: DB7PR05MB4938 Return-Path: DouglasR.Houston:-:ed.ac.uk X-OriginatorOrg: ed.ac.uk --_000_DB7PR05MB4172AC1975DD69E2607C1AE7A8410DB7PR05MB4172eurp_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCL, Does anyone know of a free (for academics at least) search tool, that will= screen a large compound library (say an SDF of 100,000 molecules) against = a reference pharmacophore/ligand, and treat the library compounds as flexib= le? Regards, _________________________________________________________________ Dr. Douglas R. Houston Senior Lecturer in Computational Biochemistry Institute of Quantitative Biology, Biochemistry and Biotechnology Room 3.12, Waddington 1 Building King's Buildings University of Edinburgh Edinburgh, EH9 3BF, UK Tel. 0131 650 7272 --_000_DB7PR05MB4172AC1975DD69E2607C1AE7A8410DB7PR05MB4172eurp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear CCL,

Does anyone know of a free (for a= cademics at least) search tool, that will screen a large compound lib= rary (say an SDF of 100,000 molecules) against a reference pharmacopho= re/ligand, and treat the library compounds as flexible?

Regards,

_________________________________________________________________

Dr. Douglas R. Houston

Senior Lecturer in Computational Biochemistry

Institute of Quantitative Biology, Biochemistry and Biotechnology

Room 3.12, Waddington 1 Building

King's Buildings

University of Edinburgh

Edinburgh, EH9 3BF, UK

Tel. 0131 650 7272

--_000_DB7PR05MB4172AC1975DD69E2607C1AE7A8410DB7PR05MB4172eurp_-- ------------=_1530701490-4310-7 Content-Type: text/plain Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Description: Edinburgh University charitable status The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ------------=_1530701490-4310-7-- From owner-chemistry@ccl.net Wed Jul 4 20:14:00 2018 From: "Cristian Bologa CBologa:salud.unm.edu" To: CCL Subject: CCL: Pharmacophore search tool Message-Id: <-53370-180704165427-28799-pH5j07/vqVrXZ0xpRDmuqg-#-server.ccl.net> X-Original-From: Cristian Bologa Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 4 Jul 2018 20:54:14 +0000 MIME-Version: 1.0 Sent to CCL by: Cristian Bologa [CBologa:+:salud.unm.edu] While you could find many tools to do that job, you might want to also have a look at ROCS from Openeye, which does both shape and pharmacophore search, and which I have used successfully in the past, alone or in combination with other tools. https://docs.eyesopen.com/rocs/shape_theory.html#color-features It is free for non-commercial academic research. https://www.eyesopen.com/academic-licensing Good luck, Cristian Cristian Bologa, Ph.D. Research Professor, Div. of Translational Informatics, Dept. of Internal Medicine, Univ. of New Mexico, School of Medicine, Innovation Discovery&Training Center, MSC09 5025, 700 Camino de Salud NE, Albuquerque, NM 87131 tel: +1 (505) 925-7534 fax:+1 (505) 925-7625 ---------------------- "If you never fail, it means you are not trying hard enough" ________________________________________ > From: owner-chemistry+cbologa==salud.unm.edu===ccl.net on behalf of HOUSTON Douglas DouglasR.Houston|ed.ac.uk Sent: Wednesday, July 4, 2018 4:51 AM To: Cristian Bologa Subject: CCL: Pharmacophore search tool [[-- External - This message has been sent from outside the University --]] To: CCL Subscribers Subject: Pharmacophore search tool Thread-Topic: Pharmacophore search tool Thread-Index: AQHUE4T0GQxaQuXz80qfuLWIz0EKhg== Date: Wed, 4 Jul 2018 10:51:26 +0000 Message-ID: References: <53363-180628160124-20553-eaQTeznx0WdaMKDErW7n+g#%#server.ccl.net> In-Reply-To: <53363-180628160124-20553-eaQTeznx0WdaMKDErW7n+g#%#server.ccl.net> Accept-Language: en-GB, en-US Content-Language: en-GB X-MS-Has-Attach: X-MS-TNEF-Correlator: authentication-results: spf=none (sender IP is ) smtp.mailfrom=DouglasR.Houston#%#ed.ac.uk; x-originating-ip: [129.215.109.1] x-ms-publictraffictype: Email x-microsoft-exchange-diagnostics: 1;DB7PR05MB4938;7:iD75O9UDzLCWON/OK8CtqMv3jVuyIh3JvreZ/OMlJI+DlV1PkBJyW/fBg0zvYZgpblgPV7YUpKdyo80VBDWbvOPwr7WOCIX2H68IqozpfzOvryakD7OJBATz7OjlUsMSzUxtr+pGoUfpqU9xGRhlPr8XvxwZ56qtlqVF9JE20cFhWpoL8CjsqOoHKTAej4zsZ46ukOMJGiovCKrGTOGV7uaZRo1oeDaTumud4bUGbT3eoJ05GFlvucxO+gZrXcBT x-ms-exchange-antispam-srfa-diagnostics: SOS; x-ms-office365-filtering-correlation-id: 7a09c876-4b2b-4d0f-6cf8-08d5e19c1794 x-microsoft-antispam: UriScan:;BCL:0;PCL:0;RULEID:(7020095)(4652040)(8989117)(4534165)(4627221)(201703031133081)(201702281549075)(8990107)(5600053)(711020)(2017052603328)(7153060)(7193020);SRVR:DB7PR05MB4938; x-ms-traffictypediagnostic: DB7PR05MB4938: x-microsoft-antispam-prvs: x-exchange-antispam-report-test: UriScan:; x-ms-exchange-senderadcheck: 1 x-exchange-antispam-report-cfa-test: BCL:0;PCL:0;RULEID:(6040522)(2401047)(8121501046)(5005006)(10201501046)(93006095)(93001095)(3231254)(944501410)(52105095)(3002001)(149027)(150027)(6041310)(20161123562045)(20161123564045)(201703131423095)(201702281529075)(201702281528075)(20161123555045)(201703061421075)(201703061406153)(20161123558120)(20161123560045)(6072148)(201708071742011)(7699016);SRVR:DB7PR05MB4938;BCL:0;PCL:0;RULEID:;SRVR:DB7PR05MB4938; x-forefront-prvs: 0723A02764 x-forefront-antispam-report: SFV:NSPM;SFS:(10009020)(366004)(396003)(39860400002)(376002)(346002)(136003)(189003)(199004)(54896002)(5660300001)(6606003)(33656002)(7116003)(8676002)(81156014)(2906002)(81166006)(7736002)(8936002)(74316002)(6436002)(6916009)(413944005)(72206003)(105586002)(55016002)(106356001)(25786009)(9686003)(478600001)(19627405001)(97736004)(74482002)(66066001)(476003)(486006)(11346002)(3846002)(6116002)(6506007)(316002)(99286004)(53936002)(2900100001)(86362001)(68736007)(786003)(446003)(256004)(5250100002)(76176011)(3480700004)(26005)(14454004)(186003)(102836004)(7696005);DIR:OUT;SFP:1101;SCL:1;SRVR:DB7PR05MB4938;H:DB7PR05MB4172.eurprd05.prod.outlook.com;FPR:;SPF:None;LANG:en;PTR:InfoNoRecords;MX:1;A:1; received-spf: None (protection.outlook.com: ed.ac.uk does not designate permitted sender hosts) x-microsoft-antispam-message-info: /n2tg3x1c3AOpGhQPmnogteMbjlQsMcohBOdNt5nDvINDSZMqSwzPFr622l8Rl1ki2E51X81dZhdGqf+RNYlOFewFdScvV1jitFbaspwG7uTJ/XUFxYFvoXBCfgtPGrvnKODKW2BKGNZ4PAlvkuKY0rMYLxRXACd6bX3bBHoUynOFrdU1DAgjEUL6mEpU5kLRG+Zmpi2dx8DE1rxNQtpVTHai1zn15XcicGi4rqixQLikzArcLzYi/iqVy/7koUW89WmSM69Ii+7Au1ESuhFr39WcRPTZOZocwCnqF7tBOUjEHEUi87ELUzhWZk808iVxqryRQiyGryiLdMdj72rFFfqfeM1vgq//qRAct5C2yk= spamdiagnosticoutput: 1:99 spamdiagnosticmetadata: NSPM Content-Type: multipart/alternative; boundary="_000_DB7PR05MB4172AC1975DD69E2607C1AE7A8410DB7PR05MB4172eurp_" MIME-Version: 1.0 X-MS-Exchange-CrossTenant-Network-Message-Id: 7a09c876-4b2b-4d0f-6cf8-08d5e19c1794 X-MS-Exchange-CrossTenant-originalarrivaltime: 04 Jul 2018 10:51:26.8063 (UTC) X-MS-Exchange-CrossTenant-fromentityheader: Hosted X-MS-Exchange-CrossTenant-id: 2e9f06b0-1669-4589-8789-10a06934dc61 X-MS-Exchange-Transport-CrossTenantHeadersStamped: DB7PR05MB4938 Return-Path: DouglasR.Houston#%#ed.ac.uk X-OriginatorOrg: ed.ac.uk --_000_DB7PR05MB4172AC1975DD69E2607C1AE7A8410DB7PR05MB4172eurp_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCL, Does anyone know of a free (for academics at least) search tool, that will= screen a large compound library (say an SDF of 100,000 molecules) against = a reference pharmacophore/ligand, and treat the library compounds as flexib= le? Regards, _________________________________________________________________ Dr. Douglas R. Houston Senior Lecturer in Computational Biochemistry Institute of Quantitative Biology, Biochemistry and Biotechnology Room 3.12, Waddington 1 Building King's Buildings University of Edinburgh Edinburgh, EH9 3BF, UK Tel. 0131 650 7272 --_000_DB7PR05MB4172AC1975DD69E2607C1AE7A8410DB7PR05MB4172eurp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable