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Past Event Listing



The available Events are listed as below:



Speaker:  JW Feng (Denali), Alberto Gobbi & Ben Sellers (Genentech), Mario Cardozo (Nurix)
 
Event Topic:  SF Bay Area COMP Together Mini-Talk Series
 
Champion:  BinQing Wei
 
Description:  Description:
Software expenditure and headcount for computational chemistry are often closely scrutinized at pharma and biotech companies. Some of us are working at smaller biotech or startups where the limitations tend to be even more severe. This meeting aims to promote sharing of strategies & tools to help address those challenges, including leveraging open-source software and cloud computing.

Schedule:

6-7pm, check-in & networking (pizza and drinks provided)

7-7:20pm, talk #1, JW Feng (Denali)
Title: Computational chemistry challenges and opportunities at a biotech startup

7:20-8pm, talk #2, Ben Sellers & Alberto Gobbi (Genentech)
Title: Chemalot and chemalot_knime versatile open source tools for many of your cheminformatics and computational chemistry tasks.

8-8:20pm, discussion moderated by Mario Cardozo (Nurix)

Notes:
Non-UCSF affiliated participants please enter through the main entrance of Genentech Hall (600 16th St., San Francisco, CA 94158) and sign in at the security desk.

Public parking is available at the UCSF Mission Bay surface lots. For more information, please visit: http://campuslifeservices.ucsf.edu/transportation/services/parking/public_parking

On-street parking is also available on 4th street and 16th street.

 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Speaker:  Eric Martin (Novartis), BinQing Wei (Genentech)
 
Event Topic:  SF Bay Area COMP Together Mini-Talk Series
 
Champion:  Siegfried Leung
 
Description:  Schedule:

6:30 – 7 pm: check-in & networking (pizza and drinks provided)

7 – 7:30 pm: Talk #1
Title: Rational Bioavailability Design: Global Sensitivity Analysis of Physiologically-Based Pharmacokinetics (GSA of PBPK)
Speaker: Eric Martin (Novartis)

7:30 – 8.00 pm: Talk #2
Title: Computational Design of Non-peptide Linkers with Restricted Protease Cleavability for Antibody-Drug Conjugates
Speaker: BinQing Wei (Genentech)

Notes:
Non-UCSF affiliated participants please enter through the main entrance of Genentech Hall (600 16th St., San Francisco, CA 94158) and sign in at the security desk.

Public parking is available at the UCSF Mission Bay surface lots. For more information, please visit:
http://campuslifeservices.ucsf.edu/transportation/services/parking/public_parking

On-street parking is also available on 4th street and 16th street.
 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Speaker:  Max Kuhn, Pfizer Ignacio Aliagas, Genentech
 
Event Topic:  Two talks on machine learning and applications in drug discovery
 
Champion:  BinQing Wei
 
Description:  6-7 pm networking over pizza & drinks

7-7:45pm 1st talk, Max Kuhn, Pfizer

Title: Under the Hood of Cubist
Abstract: Cubist model rules are a relatively unknown machine learning model that has been extensively utilized in QSAR. The model is related to work published by Ross Quinlan in the early 90’s but had remained closed source until 2010. This talk will describe the model and its mechanics and an illustrative example will be shown to demonstrate the result.

7:45-8:15pm 2nd talk, Ignacio Aliagas, Genentech

Title: The Importance of Being Earnest: Assessing Risk in Model Predictions
Abstract: QSAR models for the prediction of properties and DMPK end points can play a very important role to guide synthesis and advance compounds in the drug discovery paradigm. For prediction models to be used efficiently and with ease, integration with other modeling tools and software can facilitate their use. At the same time, it is critical to provide validation tools to quickly inform on the models’ domain of applicability within a given therapeutic project or chemical series. We describe a probabilistic approach to model prediction and how various QSAR models and validation tools are being delivered to drug discovery scientists at Genentech.

8:30pm End
 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Speaker:  Stan Krystek (BMS, New Jersey), Yipin Lu (Novartis, Emeryville)
 
Event Topic:  San Francisco Bay Area COMP Together Mini-Talks
 
Champion:  BinQing Wei
 
Description:  Please join your fellow computational chemists in San Francisco Bay Area for networking and two mini-talks.

6-7 pm: Networking & pizza

7-8:30 pm: two mini-talks
1. Stan Krystek (BMS, New Jersey)
Title: Are Antibodies the next GPCRs?
2. Yipin Lu (Novartis, Emeryville)
Title: Improve pKa predictions and inspire compound design by a carefully curated pKa Knowledgebase
 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Speaker:  Michael Grabe, Ph.D. Associate Professor University of California, San Francisco Department of Pharmaceutical Chemistry, School of Pharmacy Cardiovascular Research Institute
 
Event Topic:  San Francisco Bay Area COMP Together seminar "Advanced simulation techniques for exploring channel permeation"
 
Champion:  Hanneke Jansen
 
Description:  Please join other computational chemists in the San Francisco Bay Area for networking and a seminar. We will also take a little time to get your input on future COMP Together events.

6-7 pm: Networking & pizza

7-8 pm: Seminar

Abstract for the seminar:
Mitochondria, often called the “powerhouse of the cell”, are membrane-enclosed compartments found inside eukaryotic cells. Their primary responsibility is to convert adenosine diphosphate (ADP) to adenosine triphosphate (ATP) - a small molecule that is the main source of energy for cellular activity. The voltage-dependent anion channel (VDAC) is a protein that resides in the outer membrane of the mitochondria, and it forms the primary pathway for ADP to enter the mitochondria and ATP to exit. In the open state, more than one million ATP molecules can flow through a single VDAC channel, while the closed state blocks ATP permeation. VDAC has been studied experimentally for over 30 years, but only in the past few years have researchers determined its three dimensional structure. In this talk, I will describe our molecular simulations of VDAC in the presence of ATP to determine if the recently solved structures represent the open or closed state. Unfortunately, ATP permeation occurs on the multi-microsecond timescale, while most molecular simulations last 10-100 nanoseconds. I will discuss our use of Markov State Models to bridge these timescales by piecing together information from hundreds of short simulations to determine the long time transport behavior of the channel. If time permits, I will also discuss our recent method for using an enhanced sampling method known as Weighted Ensemble for efficiently reconstructing current-voltage curves from atomistic simulations of ion channels.
 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Event Topic:  COMP-TDT Award Celebration & Networking Event
 
Champion:  Hanneke Jansen
 
Description:  Please join us for a COMP Together networking event combined with the Award presentation for the Second TDT competition at the Fall 2014 ACS meeting in San Francisco.

Mix and mingle with friends and colleagues, hear about highlights from the Teach-Discover-Treat (TDT) initiative and celebrate the Award winners!

This informal event will be hosted on Monday August 11 at Chevys Fresh Mex on the corner of 3rd & Howard, close to the Convention Center, at 5.30 pm.

Show your ACS badge for drinks and snacks, co-sponsored by the COMP Division, Gilead and TDT sponsors.
 
Event Date/Time:  
 
Region:  National
 
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Event Topic:  COMP - TDTi networking event
 
Champion:  Hanneke Jansen
 
Description:  Please join us for a COMP - TDTi networking event, co-hosted by the COMP Division and the Teach-Discover-Treat initiative at the Fall 2013 ACS meeting in Indianapolis.

Mix and mingle with friends and colleagues, hear about highlights from the TDT initiative, including plans for round-2!

This informal event will be hosted at “the Slippery Noodle Inn” at 372 S Meridian St, just 0.2 miles from the Convention Center.

Show your ACS badge for drinks and snacks.
 
Event Date/Time:  
 
Region:  National
 
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Speaker:  Dr. Oliver Krämer, Director Structural Research, Department of Medicinal Chemistry, Boehringer Ingelheim
 
Event Topic:  Selection of Compound Subsets for Hit Identification in Cancer Drug Discovery
 
Champion:  Hanneke Jansen
 
Description:  Schedule:
6 – 6.30 pm: check-in & networking (pizza and drinks provided)
6.30 – 7.30 pm: seminar
7.30 – 8.00 pm: informal discussions & networking

Notes:
Non-UCSF affiliated participants please enter through the main entrance of Genentech Hall (600 16th St., San Francisco, CA 94158) and sign in at the security desk.

Public parking is available at the UCSF Mission Bay surface lots ($2 after 6 pm). For more information, please visit:
http://campuslifeservices.ucsf.edu/transportation/parking/public/mb/
On-street parking is also available on 4th street and 16th street.

 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Speaker:  Seth Harris, Ph.D. (Genentech), Matt Lardy, Ph.D. (Global Blood Therapeutics), Phil Payne, Ph.D. (Protein and Drug Discovery Sciences)
 
Event Topic:  SF Bay Area COMP Together Mini-Talks
 
Champion:  Siegfried Leung
 
Description:  6:00-7:00pm: Dinner and networking
7:00-7:20pm: "TTOYS: Navigating structures with a meta-data compass" Seth Harris, Ph.D. (Genentech)
7:20-7:40pm: "Automated Model Construction with the Autocorrelator" Matt Lardy, Ph.D. (Global Blood Therapeutics)
7:40-8:00pm: "Inverse Docking - A strategy to recognize large-scale receptor motion during ligand docking" Phil Payne, Ph.D. (Protein and Drug Discovery Sciences)

Location - please note it's different from the previous event at Genentech:
Genentech, Building 31, Room 1B
GPS coordinates: 37.654287, -122.382149

Driving directions:
1) drive east along E. Grand Ave., turn left onto Grandview Dr., past Carbot Rd, at the next traffic light, turn left into the parking lot.
2) drive east along Forbes Blvd, turn right onto DNA Way, go uphill past Point San Bruno Blvd, at the next traffic light, turn right into the parking lot.
Look for the sign "B-31", a new 5-story building. The conference room is on the ground floor.
 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Event Topic:  COMP Together Networking event & TDT Award presentation
 
Champion:  Hanneke Jansen
 
Description:  Monday April 8th, 5.30 to 7.30 pm

Please join us for a COMP Together networking event combined with the Award presentation for the inaugural TDT competition at the Spring 2013 ACS meeting in New Orleans.

Mix and mingle with friends and colleagues, hear about highlights from the Teach-Discover-Treat (TDT) initiative and celebrate the 4 Award winners!

This informal event will be hosted at “the District” at 711 Tchoupitoulas, just a few blocks from the Morial Convention Center.

Show your ACS badge for drinks and snacks, co-sponsored by the COMP Division and TDT.
 
Event Date/Time:  
 
Region:  National
 
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Speaker:  Roland Dunbrack, Fox Chase Cancer Center Ezra Peisach, RCSB-Protein Data Bank
 
Event Topic:  MACC Meeting - social event and lectures: Structural Bioinformatics and Protein Structure Prediction & Understanding and Interpreting PDB Data
 
Champion:  Neysa Nevins
 
Description:  RSVP to Deping Wang, deping.wang@merck.com by Fri. Mar 8. Reception at 5:30, dinner at 6.00 pm and talks begin at 7.00 pm. The lectures are free and open to the public. The cost of catered dinner is $15 payable by cash/check at the meeting. Please indicate if you plan to attend both dinner and lecture. The dinner and talks will
follow a MOE Workshop* at Bryn Mawr College held earlier in the day.

LECTURES

Roland Dunbrack
Professor, Institute for Cancer Research
Fox Chase Cancer Center
“Structural Bioinformatics and Protein Structure Prediction”
The Protein Data Bank (PDB) provides a rich source of information when viewed as a whole. Statistical analysis of structural features from atom-atom contacts to biological and crystallographic interfaces have become a branch of modern bioinformatics and computational biology. We will present results of several studies that seek to improve our understanding of protein structure and our ability to predict structure from sequence, when an experimental structure is not yet available. We have used modern non-parametric statistical methods to produce smooth and differentiable probability density estimates for backbone-dependent rotamer libraries and neighbor-residue-dependent Ramachandran maps. We have employed affinity propagation and a dihedral angle metric to cluster the conformations of the complementarity-determining regions (CDRs) of antibody loops, producing a new classification of these loops for antibody structure prediction and design. Finally, we have examined structures of homologous proteins in different crystal forms to identify likely biologically relevant interfaces. Our database, ProtCID, is a rich source of biological information on the evolution of protein-protein interactions. We have used it to identify previously unrecognized structures of autophosphorylation events of kinases.

Ezra Peisach
Research Associate/Biocurator
RCSB-Protein Data Bank
“Understanding and Interpreting PDB Data”
The Protein Data Bank (PDB) archive provides modelers access to more than 88,000 structures and 1300 folds for use in modeling, computations and more. Questions can arise from using these data, including: Is that really a water molecule in the corner of a binding site? Why is a particular side chain in one position rather than another? Does your drug candidate not appear to make the hydrogen bonds you expect? These questions all relate to the "quality" of the data you use. How "good" are the protein structures? What's the error and precision in atomic coordinates? How might you know if something is just plain wrong? Common pitfalls in use of PDB data and what the PDB archive offers beyond atomic
coordinates will be addressed. In addition, RCSB PDB resources and future wwPDB initiatives will be discussed.
The RCSB PDB is funded by NSF, NIGMS, DOE, NLM, NCI, NINDS and NIDDK and is a member of the wwPDB.

*MOE Workshop:
Mar. 13th, 9:00-5:00
Bryn Mawr College – Computer Science Lab, Park Science Center, 101 N. Merion Ave., Bryn Mawr, PA 19010
Chemical Computing Group will be offering 2 hands-on workshops at Bryn Mawr College on March 13, 2013. The workshops are free & open to the public but pre-registration is required– seats are limited.
---------------------------------------------------------------------------------------------------------------------
9:00-12:00 Protein Alignments and Homology Modeling
Sequence and structure alignments / Template selection / Building and refining homology models
13:00-17:00 Biologics Modeling and Protein Engineering
Antibody modeling/ Virtual residue scanning / Building fusion proteins / Loop grafting and conformational searching
----------------------------------------------------------------------------------------------------------------------
Both sessions are suitable for medicinal and computational chemists. For more details and to register visit: http://www.chemcomp.com/workshops.htm. CCG workshops are open to the public, so feel free to forward this email to colleagues and friends interested in the subjects presented.
Directions to Campus:
http://www.brynmawr.edu/campus/directions.shtml

 
Event Date/Time:  
 
Region:  Southern New Jersey-PA Area
 
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Speaker:  Prof. Brian Shoichet, UCSF
 
Event Topic:  Seminar/New Year social hour Talk title: Polypharmacology: A Feature, Not A Bug?
 
Champion:  BinQing Wei
 
Description:  Please join us at the 2013 kick-off seminar/social hour of Bay Area Comp Together.

Directions:
Non-UCSF affiliated participants please enter through the main entrance of Genentech Hall (600 16th St., San Francisco, CA 94158) and sign in at the security desk. Public parking is available at the UCSF Mission Bay surface lots ($2 after 6 pm). For more information, please visit:
http://campuslifeservices.ucsf.edu/transportation/parking/public/mb/
On-street parking is also available on 4th street and 16th street.

Schedule:
6 – 7 pm: check-in & networking (pizza and wine provided)
7 – 8 pm: presentation
8 – 8:30 pm: informal discussions & networking

Talk Abstract:
Protein classification typically uses structural, sequence, or functional similarity. Here we explore an organization by ligand similarity, focusing on class A GPCRs. Comparing a ligand-based and sequence-based dendograms, we identified GPCRs that were distantly linked by sequence but neighbors by ligand similarity. Experimental testing of the ligands predicted to link three of these new pairs confirmed the predicted association, with potencies ranging from the low-nanomolar to low-micromolar. We also predicted hundreds of non-GPCRs closely related to GPCRs by ligand similarity, including the CXCR2 chemokine receptor to casein kinase I, the cannabinoid receptors to epoxide hydrolase 2, and the α2 adrenergic receptor to phospholipase D, which we confirmed experimentally. Ligand similarities among these targets may reflect the conservation of identical ligands among unrelated receptors, which signal in different time domains. The method integrates these apparently unrelated receptors into chemically coherent circuits, and suggests which of these receptors may be targeted by individual ligands.

 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Speaker:  David Milward, Chief Technology Officer, Linguamatics
 
Event Topic:  Text Mining for Drug Discovery
 
Champion:  Kenneth Mattes
 
Description:  ABSTRACT
Search aims to find you documents containing keywords. Text mining aims to find knowledge hidden within documents or to synthesize knowledge from multiple documents. This talk will illustrate the wide range of questions that text mining is being used to answer across life sciences R&D based on the scientific literature and other unstructured or semi-structured data sources. This includes extracting protein-protein interactions, gene-disease relationships, mutation and expression information, biomarker relationships and quantitative information such as pharmacokinetic values. The talk will also discuss approaches which go beyond one-step relationships such as protein-protein interactions or gene diseases relationships to knowledge synthesis e.g. building profiles of compounds, targets and individuals, or automated discovery of potential mechanisms of action by combining data extracted from different documents.

The talk will conclude with a demonstration of the I2E text mining platform. This is an agile text mining platform used to extract structured information interactively from unstructured text.

DINNER RESERVATIONS:
Please go to the BAGIM website (www.BAGIM.org , preferred) or the CompTogether website (http://oldwww.acscomp.org/COMP_Together/meeting_signup.php ) to register and get additional details for the meeting at www.BAGIM.org. BAGIM will subsidize the meeting by covering both tip and tax for the meal.
 
Event Date/Time:  
 
Region:  Boston Area
 
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Speaker:  Sandor Vajda Professor of Biomedical Engineering and Chemistry Boston University
 
Event Topic:  Computational mapping of proteins for disrupting and optimizing protein-protein interactions
 
Champion:  BinQing Wei
 
Description:  Schedule:
6 – 7 pm: check-in & networking (pizza and drinks provided)
7 – 8 pm: presentation
8 – 8:30 pm: informal discussions & networking

Abstract:
Computational mapping of proteins for disrupting and optimizing protein-protein interactions

Sandor Vajda and Dima Kozakov
Departments of Biomedical Engineering and Chemistry, Boston University

Our lab developed computational solvent mapping for the identification of binding hot spots of proteins, implemented as the FTMap server (http://ftmap.bu.edu/). The method places small molecular probes, the size of organic solvents, on a dense grid around the protein, and finds the hot spots as consensus clusters formed by clusters of several probes [1]. We have shown that such hot spots can be used to identify druggable sites in protein-protein interfaces [2]. Furthermore, based on the mapping results we calculate the density of probes, which describes the binding propensity at each point. The correlation between a ligand position and the probe density yields a scoring function that can substantially improve docking, virtual screening, and design of small molecules to inhibit protein-protein interactions. These methods will be shown with application to the protein translation initiation complex eIF4F, a validated cancer target. We show that the hot spot information can also be used for solving a very different problem, i.e., selecting optimal residue mutations in the interface to increase the affinity of the interaction. The method recently provided very good results in blinded test problems of interface design (http://www.ebi.ac.uk/msd-srv/capri/round26/round26.html).

1. Brenke R, Kozakov D, Chuang G-Y, Beglov D, Hall DR, Landon MR. Mattos C, Vajda S. Fragment-based identification of druggable "hot spots" of proteins using Fourier domain correlation techniques. Bioinformatics, 25: 621–627, 2009.
2. Kozakov D, Hall DR, Chuang G-Y, Cencic R, Brenke R, Grove LE, Beglov D, Pelletier J, Whitty A, Vajda S. Structural conservation of protein hot spots in protein-protein interfaces. Proc. Nat. Acad. Sci. USA: 108: 13528-13533, 2011.
 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Speaker:  Tom Plasterer
 
Event Topic:  The Semantic Web: Semantic interoperability for drug discovery
 
Champion:  Kenneth Mattes
 
Description:  Boston Area Group for Informatics and Modeling Meeting Announcement
(www.BAGIM.org )

DATE: June 21, 2012
VENUE: The Chateau (http://www.chateaurestaurant.com/waltham/waltham.asp )
195 School Street
Waltham, MA 02451
Phone: 781.894.3339
Fax: 781.894.5291
AGENDA: 5:30-6:30 Socializing (Cash bar)
6:30 – 7:30 Dinner ( $20.00) )
7:30 - 7:45 Business meeting
7:45 – 8:30 Presentation and Q&A (open to the public)
8:30 – 9:00 Wrap-up and Departure
TITLE:
The Semantic Web: Semantic interoperability for drug discovery
SPEAKER(s):
Tom Plasterer, AstraZeneca R&D Boston

ABSTRACT
Drug discovery is transforming into an informatics-driven science. Data volume, heterogeneity, distribution, coordination and access policies are all challenges in this transformation. Many pharmaceutical companies are faced with questions such as: “Where is all of the data on a given compound?” “Is my collaborator’s concept of a given disease the same as mine?” or “How can I integrate publications and public databases with my data?”
Semantic web approaches offer solutions to these challenging questions. Using a web-scale architecture approach semantics is able to link data and metadata (data describing the data) using web standards in a common informational model termed RDF (Resource Description Framework). This model allows the linking of data elements using unique identifiers, supports higher-level concepts within the same framework and is the basis of the linked open data cloud.
The life science community has been among the early adopters of semantic technology, and has contributed over 41 linked datasets to the linked open data cloud. These datasets include biomedical repositories such as PubMed, UniProt, ChEMBL, DrugBank, LinkedCT and PDB. This talk will explore how RDF drives linked data and linked vocabularies, how applications can be built on top of this framework and will describe emerging pre-competitive efforts at sharing knowledge in the biopharma space.

Background Links
- Semantic Web organization (http://semanticweb.org/wiki/Main_Page )
- Semantic Web W3C (http://www.w3.org/2001/sw/ )
- Open PHACTS: Semantic interoperability for drug discovery (http://www.openphacts.org/)


DINNER RESERVATIONS:
Please go to the BAGIM website (www.BAGIM.org ) to register and get additional details for the meeting. BAGIM will pay the tax, tip and room fee.
 
Event Date/Time:  
 
Region:  Boston Area
 
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Speaker:  Bernd Wiswedel (Knime); Rich McClellan (Numerate); Carsten Detering (BioSolveIT); Man-Ling Lee (Genentech)
 
Event Topic:  Mini-talks about computational chemistry workflows for drug discovery Location: UCSF Byers Hall, Room 212 6 – 6.30 pm: check-in & networking (pizza and drinks provided) 6.30 – 8 pm: scientific program Bernd Wiswedel (Knime): KNIME - Integrating Data, Tools and Science Rich McClellan (Numerate): Dealing with Dirty Data with KNIME Carsten Detering (BioSolveIT): Using KNIME and PipelinePilot to fuzzily search in available chemistry - and beyond Man-Ling Lee (Genentech): Unix Pipe Revival at Genentech 8 – 8.30 pm: informal discussions & networking
 
Champion:  Hanneke Jansen
 
Description:  Non-UCSF affiliated participants please enter through the main entrance of Genentech Hall (600 16th St., San Francisco, CA 94158) and sign in at the security desk.

Public parking is available at the UCSF Mission Bay surface lots ($2 after 6 pm). For more information, please visit:
http://campuslifeservices.ucsf.edu/transportation/parking/public/mb/
On-street parking is also available on 4th street and 16th street.
 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Speaker:  Bernd Wiswede, KNIME.com AG, (http://www.knime.org/) Alain Deschenes, Chemical Computing Group (http://www.chemcomp.com/)
 
Event Topic:  KNIME - Integrating Data, Tools and Science and Interfacing MOE and KNIME
 
Champion:  Kenneth Mattes
 
Description:  AGENDA: 5:30-6:30 Socializing (Cash bar)
6:30 – 7:30 Dinner ($30.00, or $25.00 for students and post-docs)

7:30 - 7:45 Business meeting
7:45 – 8:45 Presentation and Q&A (open to the public)
8:45 – 9:30 Wrap-up and Departure

ABSTRACT
KNIME (Konstanz Information Miner) is a user-friendly and comprehensiveopen-source data integration, processing, analysis, and exploration platform. Its visual workbench combines data access, data transformation, initial investigation, powerful predictive analytics and visualization. Through its open API KNIME also acts as an integration backbone for a variety of tools. In just a few years, a number of open source (Weka, R, CDK) but also commercial integrations (such as provided by the Chemical Computing Group) have already appeared within KNIME adding a wealth of domain specific functionality. This talk will give an introduction to KNIME, showcase some of the community and commercial vendor contributions (particularly in the chem-informatics space) and outline some of the extensions available for KNIME that enable the deployment in a corporate environment.
CCG has been actively developing a MOE interface in KNIME since 2007. The current offering contains over 100 nodes supporting 18 data types covering a wide range of life science areas, such as ligand-based and structure-based modeling, cheminformatics, and QSAR. Combining MOE with KNIME brings data mining to modeler’s desktop in an easy to use fashion. This talk will discuss the interface architecture, the introduction of support for the MOE/soap server, the node development kit, the breadth of currently available nodes and how they can be obtained. Sample workflows highlighting how research teams can benefit from interfacing MOE with KNIME.

DINNER RESERVATIONS:
Please go to the BAGIM website (www.BAGIM.org ) to register and get additional details for the meeting.

NOTES:
(1) Complimentary parking will be available upon request (up to 20 spaces available)
(2) CCG will be conducting workshops earlier during the day at the same location (09:00 AM - Structure-Based Drug Design: Ligand optimization in the pocket & 1:00 PM - Protein Modeling:
Structure preparation | Loop grafting | Conformational searching). For those interested in attending, registration is open at http://www.chemcomp.com/workshops.htm
 
Event Date/Time:  
 
Region:  Boston Area
 
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Event Topic:  COMP Together networking and social hour at the 2012 ACS San Diego Meeting
 
Champion:  Sara Nichols
 
Description:  Monday, March 26th from 6-8pm

Please join us as we kick-off the first COMP Together networking and social hour at a national ACS meeting.
Mix and mingle with friends and colleagues in academia and industry, and hear about highlights from the Teach-Discover-Treat (TDT) initiative by COMP members.

This informal event will be hosted at the Rock Bottom Brewery in downtown San Diego at 401 G Street, located on the corner of G and 4th (roughly 5 blocks from the San Diego Convention Center).

Food and beverages will be provided with a cash bar, sponsored by Accelrys and Schrödinger.

All are welcome!
 
Event Date/Time:  
 
Region:  National
 
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Speaker:  Robert Abel (Schrodinger); Jean Francois Truchon (Chemical Computing Group); Matt Geballe (OpenEye)
 
Event Topic:  Scientific talks & a panel discussion focusing on these new tools to assess the effect of solvation on ligand-protein interactions: WaterMap (Schrodinger), 3D-RISM (CCG), and SZMAP (OpenEye).
 
Champion:  BinQing Wei
 
Description:  Room: in Building #2 ( the center one with visitor desk)

Event Agenda:
6-6:30pm check-in/dinner
6:30-7pm Robert Abel (Schrodinger)
Title: The role of the solvent in protein-ligand binding: applications to druggability and ligand design
7-7:30pm Jean Francois Truchon (Chemical Computing Group)
Title: Integral Equation Theory: A Rigorous Way to Treat Solvent Free Energy
7:30-8pm Matt Geballe (OpenEye)
Title: TBD
8-8:30pm Panel discussion
 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Speaker:  Drs. Zsolt Zsoldos and Orr Ravitz, SimBioSys Inc (
 
Event Topic:  Family based scoring and docking constraints in eHiTS
 
Champion:  Kenneth Mattes
 
Description:  Boston Area Group for Informatics and Modeling Meeting Announcement
(www.BAGIM.org )

DATE: January 19, 2012

VENUE: Elephant Walk in Cambridge (free parking and meeting room) (http://www.elephantwalk.com/cambridge/index.html )
2067 Massachusetts Avenue, Cambridge, MA 02140
617-492-6900

AGENDA: 5:30-6:30 Socializing (Cash bar)
6:30 – 7:30 Dinner (3 course, $30.00)
)
7:30 - 7:45 Business meeting
7:45 – 8:30 Presentation and Q&A (open to the public)
8:30 – 9:00 Wrap-up and Departure

TITLE:
Family based scoring and docking constraints in eHiTS

SPEAKER(s):
Drs. Zsolt Zsoldos and Orr Ravitz, SimBioSys Inc (http://www.simbiosys.ca/)

ABSTRACT
eHiTS uses a novel, statistical knowledge-based scoring method consisting of interacting surface points and physical terms combined with an adaptive parameter scheme. This approach offers users the capability to fine-tune the scoring function using their data and thus incorporate their full body of knowledge in a systematic and automatic fashion.
(See recent paper: > http://www.springerlink.com/content/r1t66167718h5110/
> DOI: 10.1007/s10822-011-9482-5 )
Prior to the talk, a short overview of the CLiDE program will be given. CLiDE is a tool for extraction of chemical structures from documents and images. The program is capable of transforming 2D molecular depictions into standard chemical file formats, and it interfaces with the major chemical editors. The technical and scientific challenges of perceiving chemistry from images of varied qualities and representation conventions will be discussed, and examples for how those issues are addressed by CLiDE will be given. We will show how the different versions of CLiDE meet the different needs of chemists, as well as of IT and IP professionals constructing chemical databases from publications, patents, and reports

DINNER RESERVATIONS:
Please go to the BAGIM website (www.BAGIM.org , preferred) or the CompTogether website (http://oldwww.acscomp.org/COMP_Together/meeting_signup.php )to register and get additional details for the meeting at www.BAGIM.org. BAGIM will subsidize the meeting by covering both tip and tax for the meal.
 
Event Date/Time:  
 
Region:  Boston Area
 
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Speaker:  Suggested Discussion Topic for Social Event
 
Event Topic:  The Automated Topology Builder (ATB) and Repository
 
Champion:  Kenneth Mattes
 
Description:  Comp-Together / BAGIM Announcement
(http://oldwww.acscomp.org/COMP_Together/meeting_signup.php /
Or www.BAGIM.org )

DATE: December 6, 2011

VENUE: The Chateau Restaurant in Waltham
(http://www.chateaurestaurant.com/ )
195 School Street, Waltham, MA 02451
781.894.3339

AGENDA: 5:30-7:30 Socializing (Cash bar) and Topic Discussion
7:30-8:30 Stay for Dinner (at your expense)?
RSVP: by December 5, to Ken Mattes (ken.mattes@astrazeneca.com ) 781-839-4649
http://oldwww.acscomp.org/COMP_Together/meeting_signup.php /
Or www.BAGIM.org

OPTIONAL DISCUSSION TOPIC (You can bring your own too!):
The Automated Topology Builder (ATB) and Repository (DOI: 10.1021/ct200196m)
• http://compbio.biosci.uq.edu.au/atb/?tab=builder_tab
• http://compbio.biosci.uq.edu.au/atb/
Abstract
The Automated force field Topology Builder (ATB, http://compbio.biosci.uq.edu.au/atb) is a Web-accessible server that can provide topologies and parameters for a wide range of molecules appropriate for use in molecular simulations, computational drug design, and X-ray refinement. The ATB has three primary functions: (1) to act as a repository for molecules that have been parametrized as part of the GROMOS family of force fields, (2) to act as a repository for pre-equilibrated systems for use as starting configurations in molecular dynamics simulations (solvent mixtures, lipid systems pre-equilibrated to adopt a specific phase, etc.), and (3) to generate force field descriptions of novel molecules compatible with the GROMOS family of force fields in a variety of formats (GROMOS, GROMACS, and CNS). Force field descriptions of novel molecules are derived using a multistep process in which results from quantum mechanical (QM) calculations are combined with a knowledge-based approach to ensure compatibility (as far as possible) with a specific parameter set of the GROMOS force field. The ATB has several unique features: (1) It requires that the user stipulate the protonation and tautomeric states of the molecule. (2) The symmetry of the molecule is analyzed to ensure that equivalent atoms are assigned identical parameters. (3) Charge groups are assigned automatically. (4) Where the assignment of a given parameter is ambiguous, a range of possible alternatives is provided. The ATB also provides several validation tools to assist the user to assess the degree to which the topology generated may be appropriate for a given task. In addition to detailing the steps involved in generating a force field topology compatible with a specific GROMOS parameter set (GROMOS 53A6), the challenges involved in the automatic generation of force field parameters for atomic simulations in general are discussed.
 
Event Date/Time:  
 
Region:  Boston Area
 
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Speaker:  Michael Chimenti (UCSF), Alan Cheng (Amgen) and Da
 
Event Topic:  Dinner + 3 Mini-Talks: 6-6:30pm: Social + dinner 6:30-6:50: Michael Chimenti (UCSF): The central role of pH sensing proteins in cancer cell adap
 
Champion:  Vickie Tsui
 
Description:  Non-UCSF affiliated participants please enter through the main entrance of Genentech Hall (600 16th St., San Francisco, CA 94158) and sign in at the security desk.

Public parking is available at the UCSF Mission Bay surface lots ($2 after 6 pm). For more information, please visit:
http://campuslifeservices.ucsf.edu/transportation/parking/public/mb/
On-street parking is also available on 4th street and 16th street.
 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Speaker:  Uli Schmitz, Ph.D. (Gilead), Jianwen Feng, Ph.D. (
 
Event Topic:  SF Bay Area COMP Together Mini-Talk Series
 
Champion:  Siegfried Leung
 
Description:  6-6:30pm: Dinner and networking

6:30-6:50pm: "Keeping track of the competition" Uli Schmitz

6:50-7:10pm: "Interactive Shape and Pharmacophore Similarity Search" Jianwen Feng

7:10-7:30pm: "Boltzmann-weighted conformational profiling in the design of ligands with improved potency" John Eksterowicz

7:30-8pm: Discussions and networking
 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Event Topic:  COMP Mentor Lunches in Denver (Academic Lunch)
 
Champion:  Rommie Amaro
 
Description:  Are you interested to network with other COMP chemists and/or learn about what it’s like to work in industrial and academic environments? Will you be attending the upcoming national meeting in Denver?

If so, make the most of your annual meeting experience and join us for our COMP mentor lunches. Enjoy a free lunch and the opportunity to network!

Please join us in Denver, where we will offer an academic mentor lunch and an industrial mentor lunch on Tuesday, August 30 at noon. Groups will meet outside the COMP symposia and then depart for lunch at a local restaurant. Lunches are limited to the first 10 people who sign up; sign-ups are done through the COMP Together website.

COMP Mentor Lunches
As part of our ongoing initiative to bring computational chemists together and provide new venues for networking, COMP offers the possibility for junior members to have lunch with senior researchers at the national meetings. The goal is to allow for networking in an open, relaxed setting and to promote discussions about possible career paths in academia and industry. Academic mentees will be able to meet with professors and receive application and interview tips in time for the upcoming academic recruiting season. Industrial mentees can network and get the inside scoop on what it’s like to work in industry. All are welcome.

We also welcome and encourage COMP members to become part of the COMP mentor network as industrial or academic mentors. Please contact Rommie Amaro ( ramaro@uci.edu ) if you are interested in being a COMP mentor or with general questions about COMP mentoring initiatives.
 
Event Date/Time:  
 
Region:  National
 
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Email:

 

 

Event Topic:  COMP Mentor Lunches in Denver (Industrial Lunch)
 
Champion:  Rommie Amaro
 
Description:  Are you interested to network with other COMP chemists and/or learn about what it’s like to work in industrial and academic environments? Will you be attending the upcoming national meeting in Denver?

If so, make the most of your annual meeting experience and join us for our COMP mentor lunches. Enjoy a free lunch and the opportunity to network!

Please join us in Denver, where we will offer an academic mentor lunch and an industrial mentor lunch on Tuesday, August 30 at noon. Groups will meet outside the COMP symposia and then depart for lunch at a local restaurant. Lunches are limited to the first 10 people who sign up; sign-ups are done through the COMP Together website.

COMP Mentor Lunches
As part of our ongoing initiative to bring computational chemists together and provide new venues for networking, COMP offers the possibility for junior members to have lunch with senior researchers at the national meetings. The goal is to allow for networking in an open, relaxed setting and to promote discussions about possible career paths in academia and industry. Academic mentees will be able to meet with professors and receive application and interview tips in time for the upcoming academic recruiting season. Industrial mentees can network and get the inside scoop on what it’s like to work in industry. All are welcome.

We also welcome and encourage COMP members to become part of the COMP mentor network as industrial or academic mentors. Please contact Rommie Amaro ( ramaro@uci.edu ) if you are interested in being a COMP mentor or with general questions about COMP mentoring initiatives.
 
Event Date/Time:  
 
Region:  National
 
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Email:

 

 

Event Topic:  ACS COMP Together - Connecticut Networking/Social Event
 
Champion:  Veerabahu (Veer) Shanmugasundaram
 
Description:  You are cordially invited you to a
ACS COMP Together – Connecticut Networking/Social Event
sponsored by the ACS COMP Division

on
Thursday, August 25th
5:00-7:00PM

at
Leon's Restaurant
http://www.leonsrestaurant.com/
501 Long Wharf Dr, New Haven, CT – 06511

ACS COMP Together CT Local Champions
Dave Beveridge – Wesleyan
Erin Duffy - Rib-X
Ingo Mugge – Boehringer Ingelheim
Jayaraman Chandrasekhar – Gilead
Julian Tirado-Rives - Yale
Mark Gerstein - Yale
Martha Grossel - Conn College
Ram Rajamani - BMS
Veer Shanmugasundaram - Pfizer
 
Event Date/Time:  
 
Region:  Connecticut
 
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Speaker:  Jacob Corn, Ph.D. (Scientist, Genentech)
 
Event Topic:  Seminar Presentation: "Macromolecular modeling and design with Rosetta"
 
Champion:  Vickie Tsui
 
Description:  6-6:30pm: Dinner and networking
6:30-7:30pm: Seminar
7:30-8pm: Discussions and networking

Please follow the map below and sign in at the Building 14 lobby:

http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=340+Pt.+San+Bruno+Blvd+South+San+Fransisco,+CA,+94080
 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Event Topic:  Happy Hour Networking.
 
Champion:  Samuel Toba
 
Description:  Network with your local COMP and CINF colleagues.

RiRa Irish Pub
4931 Elm Street
Bethesda, MD 20814-2905
(301) 657-1122
www.rira.com/rira/bethesda.html
 
Event Date/Time:  
 
Region:  Washington DC - Northern VA
 
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Event Topic:  COMP Together San Diego Kick-off Event
 
Champion:  Rommie Amaro
 
Description:  6:00 - 9:00 PM Social hours and networking. Food and beverages will be provided, with a cash bar.

Please join us as we kick-off the San Diego region's COMP Together networking initiative with an informal networking and social event at the Rock Bottom Brewery in La Jolla.

All are welcome!
 
Event Date/Time:  
 
Region:  San Diego
 
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Event Topic:  San Francisco Bay Area COMP Together May Networking Event
 
Champion:  Hanneke Jansen
 
Description:  Come join other computational chemists in the San Francisco Bay Area for networking and to provide feedback on the COMP Together initiative. We are looking for your ideas to shape our next events !

We have not yet determined the location for this event but it will be somewhere in a BART-accessible bar in San Francisco. This is a no-host event or as some people would say "a Dutch treat". In other words, plan to pay for your own food & drinks.

Please RSVP so we can get a head-count and make arrangements accordingly.

Your San Francisco Bay Area champions,
Hanneke, Vickie & Siegfried
 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Speaker:  Jean-Franois Truchon, Ph.D., Research Scientist,
 
Event Topic:  How integral equation theory fits into the drug discovery picture: the solvent slush
 
Champion:  Kenneth Mattes
 
Description:  AGENDA: 5:30-6:00 Socializing (Cash bar)
6:00-7:00 Dinner ($25.00)
7:00-8:00 Presentation (open to the public)
8:00-8:30 Q&A session

ABSTRACT
Integral equation theories are mathematically derived from statistical mechanics and constitute an accurate middle ground between molecular dynamics (MD) and Poisson-Boltzmann methods. Not only does this class of theory correctly give access to thermodynamic quantities, but they also link them to explicit particle distributions. We have recently been investigating a particular flavor - 3D-RISM/KH - looking for insights into the role of solvent and salts in the ligand binding event. We present preliminary results on small molecule free energies of solvation, prediction of bridging water positions, and the distribution of salt and water in active sites and protein cavities.

DINNER RESERVATIONS:
Please go to the BAGIM website (www.BAGIM.org ) to register
Alternatively go to the Comp. Together website

DINNER SELECTION:
FIRST COURSE

GRAFTON GREEN SALAD
MESCLUN, CRISPY SHALLOTS, RED GRAPES AND GREAT HILL BLUE CHEESE

ENTRE COURSE (Select one)

ROASTED BISTRO CHICKEN
ROASTED CHICKEN, CHIVE MASHED POTATO,
LEMONY WATERCRESS, SAGE BROWN BUTTER

GRILLED MEYER RANCH HANGER STEAK
SAUTEED SPINACH, CHIVE MASHED POTATO, SAUCE BORDELAISE

BUTTERNUT SQUASH RAVIOLI
WITH A BROWN BUTTER SAUCE, GARNISHED WITH ARUGULA

(REGULAR AND DECAF COFFEE, TEA ARE INCLUDED, DESSERT EXTRA)
 
Event Date/Time:  
 
Region:  Boston Area
 
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Speaker:  Matthew P. Jacobson, Ph.D., UCSF
 
Event Topic:  SF Bay Area COMP Together Seminar Series - "Structure-based ADME prediction"
 
Champion:  Siegfried Leung
 
Description:  6-7 pm: Social hour (Food and beverages are provided)

7-8 pm: Keynote Speaker

Non-UCSF affiliated participants please enter through the main entrance of Genentech Hall (600 16th St., San Francisco, CA 94158) and sign in at the security desk.

Public parking is available at the UCSF Mission Bay surface lots ($2 after 6 pm). For more information, please visit:
http://campuslifeservices.ucsf.edu/transportation/parking/public/mb/
On-street parking is also available on 4th street and 16th street.
 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Email:

 

 

Event Topic:  COMP Mentor Lunches
 
Champion:  Rommie Amaro
 
Description:  Please join us at the national meeting in Anaheim, where we will offer an academic mentor lunch and an industrial mentor lunch on Tuesday, March 29 at noon. The goal is to allow for networking in an open, relaxed setting and to promote discussions about possible career paths in academia and industry. All are welcome. Groups will meet outside the COMP symposia and then depart for lunch at a local restaurant. When registering through the web, please indicate in the comment field whether you're registering for the academic or the industrial lunch. Additional sign-up sheets will be available outside of the COMP symposia.
 
Event Date/Time:  
 
Region:  National
 
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Speaker:  Michael S. Lajiness, Ph.D., Eli Lilly & Co
 
Event Topic:  SF Bay Area COMP Together Seminar Series - "Structure-Activity Landscape Analysis and Variation"
 
Champion:  Vickie Tsui
 
Description:  6-7 pm: Poster viewing and social hour (pizza and beverages are provided)
Poster presenters:
Xiaowu Chen, Gilead
Michael Chimenti, UCSF
Christian Laggner, UCSF
David Spellmeyer, Nodality
Patrick Weinkam, UCSF

7-8 pm: Keynote Speaker
 
Event Date/Time:  
 
Region:  SF Bay Area
 
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Speaker:  Carsten Detering
 
Event Topic:  Juggling billions of compounds by modern fragment based lead design
 
Champion:  Kenneth Mattes
 
Description:  Abstract:
> A much more rationale approach than screening full compounds and then
> stripping down low molecular hitters to build them up again, is to
> work with fragments from the ground up. Moreover, fragments give
> inherently more possibilities in piecing together available chemistry
> than fully enumerated compound sets.
> If the fragments used in an in silico approach stem from in house
> chemical building blocks, and are connected according to in house
> chemical protocols, the IP stays within a company's boundaries, and
> the compounds can also be synthesized a lot quicker than with external
> building blocks.
> Further, bringing medicinal chemists in front of the computer along
> with the computational chemists, a lot of design steps can be saved in
> an iterative process, where the chemist gives immediate feedback on
> the synthesizality of the compounds found.
> We will show the science behind a few applications which address all
> the above mentioned advantages of fragment based lead discovery.
 
Event Date/Time:  
 
Region:  Boston Area
 
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The views and opinions expressed in this page are strictly those of the Division of Computers in Chemistry. The contents of this page have not been reviewed or approved by the American Chemical Society. Please address all comments and other feedback to the the COMP Division.

This page was last modified 07:03:48, June 3, 2015