MrBUMP: progress and plans

Slides:

Advertisements

Similar presentations

Making the System Operational

Advertisements

Molecular Replacement in CCP4

Molecular Replacement

M.D.Winn, DL, March 28th 2007 Session 4 Core activities Intro Overview: Martyn CCP4 Releases: Charles Installation issues: Francois Meetings: Maeri Python.

Clustal W and Clustal X version 2.0 김영호, 박준호, 최현희 The 9 th Protein Folding Winter School.

Prediction to Protein Structure Fall 2005 CSC 487/687 Computing for Bioinformatics.

A Molecular Replacement Pipeline Garib Murshudov Chemistry Department, University of York 

Tertiary protein structure viewing and prediction July 5, 2006 Learning objectives- Learn how to manipulate protein structures with Deep View software.

Detecting the Domain Structure of Proteins from Sequence Information Niranjan Nagarajan and Golan Yona Department of Computer Science Cornell University.

SYSTEM CENTER: ENDPOINT PROTECTION FUNDAMENTALS Howard A. Carter III Senior Consultant Microsoft Consulting Services September 21, 2013 TechGate 2013 –

MODELLER hands-on Ben Webb, Sali Lab, UC San Francisco Maya Topf, Birkbeck College, London.

Protein domains. Protein domains are structural units (average 160 aa) that share: Function Folding Evolution Proteins normally are multidomain (average.

CCP4 Study Weekend 3rd January 2003 CCP4i - “Tricks and Tools” Peter Briggs CCP4 Daresbury.

Peter J. Briggs, Liz Potterton *, Pryank Patel, Alun Ashton, Charles Ballard, Martyn Winn CLRC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, UK *

28 th March 2007 MrBUMP – Automated Molecular Replacement Ronan Keegan, Martyn Winn CCP4, Daresbury Laboratory.

28 Mar 06Automation1 Overview of developments within CCP4 Generation 1 ccp4i tasks Generation 2 isolated scripts / web service Generation 3 integrated.

Molecular Replacement Martyn Winn CCP4 group, Daresbury Laboratory, UK.

Authors Project Database Handler The project database handler dbCCP4i is a small server program that handles interactions between the job database and.

A Molecular Replacement Pipeline Garib Murshudov Chemistry Department, University of York 

TEAM Basic TotalElectrostatic ManagementAwareness&

A Molecular Replacement Pipeline Garib Murshudov Chemistry Department, University of York 

BALBES (Current working name) A. Vagin, F. Long, J. Foadi, A. Lebedev G. Murshudov Chemistry Department, University of York.

23 rd March 2005CCP4 Annual Developers’ Meeting 1 DL: Releases, Conferences and Other Activities Peter Briggs, CCP4 Daresbury.

Portal User Group Meeting June 13, Agenda I. Welcome II. Updates on the following: –Migration Status –New Templates –DB Breakup –Keywords –Streaming.

EBI is an Outstation of the European Molecular Biology Laboratory. Annotation Procedures for Structural Data Deposited in the PDBe at EBI.

Porto, 4-5 March, 1999 The COST250 Speaker Recognition Reference System H. Melin, A.M. Ariyaeeinia, M. Falcone.

MolIDE2: Homology Modeling Of Protein Oligomers And Complexes Qiang Wang, Qifang Xu, Guoli Wang, and Roland L. Dunbrack, Jr. Fox Chase Cancer Center Philadelphia,

Bulk Model Construction and Molecular Replacement in CCP4 Automation Ronan Keegan, Norman Stein, Martyn Winn.

R. Keegan 1, J. Bibby 3, C. Ballard 1, E. Krissinel 1, D. Waterman 1, A. Lebedev 1, M. Winn 2, D. Rigden 3 1 Research Complex at Harwell, STFC Rutherford.

MrBUMP – Molecular Replacement with Bulk Model Preparation Automated search model discovery and preparation for structure solution by molecular replacement.

Systems Analysis and Design in a Changing World, Fourth Edition

Developments with CCP4i & the Database Handler Peter Briggs.

Protein Tertiary Structure. Protein Data Bank (PDB) Contains all known 3D structural data of large biological molecules, mostly proteins and nucleic acids:

Data Harvesting: automatic extraction of information necessary for the deposition of structures from protein crystallography Martyn Winn CCP4, Daresbury.

Having a Blast! on DiaGrid Carol Song Rosen Center for Advanced Computing December 9, 2011.

1 MrBUMP – Molecular Replacement with Bulk Model Preparation Ronan Keegan, Martyn Winn CCP4 group, Daresbury Laboratory Como May 23rd 2006.

Shawn Jones INDUS Corporation January 18, 2000 Open Forum on Metadata Registries Santa Fe, NM SDC JE-2029.

Sequence Based Analysis Tutorial March 26, 2004 NIH Proteomics Workshop Lai-Su L. Yeh, Ph.D. Protein Science Team Lead Protein Information Resource at.

SR Users Meeting 10-11th September 2003 CCP4 Release 5.0 Peter Briggs CCP4/CCLRC Daresbury Laboratory.

M.D.Winn, York, March 22nd/23rd 2005 CCP4 Library Development.

17 th March 2008 MrBUMP progress report Ronan Keegan & Martyn Winn Daresbury Laboratory.

CCP4 Molecular Replacement Model Generation Create a CCP4i task for generating Molecular Replacement models. - Selecting suitable PDB entries, based on.

EBI is an Outstation of the European Molecular Biology Laboratory. PDBe Search Services (PDBelite, PDBePro and BIObar) Sanchayita Sen, Ph.D. PDB Depositions.

HANDS-ON ConSurf! Web-Server: The ConSurf webserver.

Workshop U.S. Nuclear Regulatory Commission Rockville, Maryland Pacific Northwest National Laboratory November 15-17, 2005 Constituent Data Editor.

Peter J. Briggs, Alun Ashton, Charles Ballard, Martyn Winn and Pryank Patel CCLRC Daresbury Laboratory, Warrington, Cheshire WA4 4AD, UK The CCP4 project.

What does the future hold? SAPHIRE CCP4 libraries Program Developments More automation 3D viewer Project CCP4 Study Weekend 2003 BAR!

Aleksandra Pawlik University of Manchester. Something that can be put into a workflow Well described - what the component does Behaves “well” - conforms.

Aleksandra Pawlik Alan Williams University of Manchester.

Tools For Vertebrate Gene Naming

1. Open any Office 2016 app, such as Word, and create a new document.

CCP4 6.1 and beyond: Tools for Macromolecular Crystallography

Fastdroid Produced by : Firas Abdalhaq Mohammad Amour Supervised by : Dr. Raed Alqadi.

Complete automation in CCP4 What do we need and how to achieve it?

Review of CCP4 Release 5.0 Peter Briggs CCP4

Project tracking system for the structure solution software pipeline

Releases, Conferences and Other Activities

Sequence Based Analysis Tutorial

Configuration Of A Pull Network.

Progress Report in REFMAC

Protein structure prediction.

Core Activities Review of 06/07 Plans for 07/08 29 Mar 05 Review.

CCLRC Daresbury Laboratory

DSC Governance Sub Group Recommendations

Automated Molecular Replacement

TargetDB and PEPCDB •

The temporary site to download BALBES:

NIEM Tool Strategy Next Steps for Movement

The site to download BALBES:

From STAB teleconference minutes

Presentation transcript:

MrBUMP: progress and plans Ronan Keegan, Martyn Winn CCP4 group CCLRC Daresbury Laboratory M.D.Winn, York, March 28th 2006

Progress since last automation meeting Basic scheme unchanged - consolidation and new options New techniques: Addition of SCOP domains to list of templates Multiple alignment of hits with CLUSTALW or MAFFT Addition of polyALA model to list of model generation techniques (PDBSET) Selected download of PDB files - faster Network dependence: Initial FASTA search can be done locally if program available Remaining dependence: update of search database files, download of coordinate files, download of .mmol files M.D.Winn, York, March 28th 2006

Progress since last automation meeting (cont) Public beta release: 5th January 2006 compulsory dependencies: mafft/clustalw, gnuplot simple installation, including ccp4i interface several updates since then, announced via www.ccp4.ac.uk/martyn/BMP/mrbump.php feedback: minor problems and some successes reported (how many unreported?) M.D.Winn, York, March 28th 2006

Progress since last automation meeting (cont) User options: Generate search models only Display assumed spacegroup User control over: Number of clashes tolerated in Phaser Number of Refmac cycles Chain IDs to definitely include Context-dependent list of references displayed M.D.Winn, York, March 28th 2006

Future plans - short-term Windows port Replace PQS with PISA: Give a list of possible multimers with scores User-specified spacegroup M.D.Winn, York, March 28th 2006

Future plans - long-term Improved alignment: Multiple alignment against larger sequence database Alignment from profile-based search User-supplied alignment Complexes: Input of multiple target sequences Model generation: Identification of flexible loops Normal mode generated conformations M.D.Winn, York, March 28th 2006