salilab.org

Andrej Sali Lab

Bull; Lab Members. Bull; Research Positions. Bull; Directions and Maps. Bull; Lab Pages. Bioinformatics, Computational Structural Biology. We are using computation grounded in the laws of physics and evolution to study the structure and function of proteins. We aim to improve and apply methods for:. Predicting the structures of proteins;. Determining the structures of macromolecular assemblies;. Annotating the functions of proteins using their structures. Congratulations to Jeremy Horst:. The paper "Stru...

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Andrej Sali Lab | salilab.org Reviews

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Bull; Lab Members. Bull; Research Positions. Bull; Directions and Maps. Bull; Lab Pages. Bioinformatics, Computational Structural Biology. We are using computation grounded in the laws of physics and evolution to study the structure and function of proteins. We aim to improve and apply methods for:. Predicting the structures of proteins;. Determining the structures of macromolecular assemblies;. Annotating the functions of proteins using their structures. Congratulations to Jeremy Horst:. The paper Stru...

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Andrej Sali Lab | salilab.org Reviews

https://salilab.org

Bull; Lab Members. Bull; Research Positions. Bull; Directions and Maps. Bull; Lab Pages. Bioinformatics, Computational Structural Biology. We are using computation grounded in the laws of physics and evolution to study the structure and function of proteins. We aim to improve and apply methods for:. Predicting the structures of proteins;. Determining the structures of macromolecular assemblies;. Annotating the functions of proteins using their structures. Congratulations to Jeremy Horst:. The paper "Stru...

INTERNAL PAGES

salilab.org

1

Andrej Sali Lab

http://salilab.org/npc.html

Bull; Lab Members. Bull; Research Positions. Bull; Directions and Maps. Bull; Lab Pages. Determining the architectures of macromolecular assemblies. This page lists some of the commentaries on our recent papers about a method to determine the structures of macromolecular assemblies and its application to the nuclear pore complex. 450, 683-694, 2007. 450, 695-701, 2007. These two NPC papers where highlighted in:. The favorite cell biology paper in 2007, selected by Nature editors, This year in Nature.

2

About MODELLER

http://salilab.org/modeller

For most Unix/Linux systems, Windows, and Mac. Several graphical interfaces to MODELLER are commercially available. There are also many other resources and people using Modeller. In graphical or web interfaces or other frameworks. B Webb, A. Sali. Comparative Protein Structure Modeling Using Modeller. Current Protocols in Bioinformatics, John Wiley and Sons, Inc., 5.6.1-5.6.32, 2014. The current release of Modeller is 9.17.

3

DBAli v2.0 home page

http://salilab.org/DBAli

Oct 6th, 2007. 06/17/08 - The DBAli database is no longer being updated. The PDB has recently released. A new version of the remediated PDB files. In order to adapt all the DBAli scripts and programs (currently more than 13,000 Perl lines and more than 5,000 PHP lines), we have decided to stop the updates until all the code is verified to properly work with the new PDB files. DBAli A Database of Structure Alignments. Marc A. Marti-Renom. And A Ortiz's MAMMOTH. Use the links from the left frame to:.

4

Download & Installation

http://salilab.org/modeller/download_installation.html

MODELLER is available free of charge to academic non-profit institutions; you will, however, need to register for a license. In order to use the software. It is also available through Accelrys. For government research labs and commercial entities. Modeller 9.17, released Jul. 7th, 2016. Mac (32-bit or 64-bit Intel). Package is also available. Linux (64-bit x86 64 RPM). Linux (32-bit Debian/Ubuntu package). Linux (64-bit x86 64 Debian/Ubuntu package). And a copy of GNU Privacy Guard (GPG).

5

About MODELLER

http://salilab.org/modeller/modeller.html

For most Unix/Linux systems, Windows, and Mac. Several graphical interfaces to MODELLER are commercially available. There are also many other resources and people using Modeller. In graphical or web interfaces or other frameworks. B Webb, A. Sali. Comparative Protein Structure Modeling Using Modeller. Current Protocols in Bioinformatics, John Wiley and Sons, Inc., 5.6.1-5.6.32, 2014. The current release of Modeller is 9.17.

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grahamjlab.org

Collaborations - Mesoscope @ UCSF

http://www.grahamjlab.org/collaborations

SciViz Careers and Tools. VIZBI 2013 uPy/ePMV/autoPACK Workshop. Johns Hopkins Workshop 2013. AMI ePMV workshop 2013. Behold HIV-1 0.1.6. Best Blender Animation Ever (uses ePMV too! HHMI illustration brought back to life. Immune Defense kickstarter 16 days. Johnson wins 2nd place Biophysical Society Annual Meeting 2014 Image Contest. Lecture at Faraday Discussion 169 in May, 2014. Lecture: Sampson Feldman Visiting Scholar. Ritisha Laungani receives Allan Kuchinsky Student Award. SciViz Careers and Tools.

whitelab.net

Interesting Links

http://www.whitelab.net/page3/page3.html

The White Lab @ DrexelMed. Department of Biochemistry & Molecular Biology, Drexel University College of Medicine. Ligand-gated Ion Channel Database. Michael Sternberg's Structural Bioinformatics group. Andrej Sali's Lab- Computational Structural Biology. NIH Office of Extramural Research. NIH Study Section rosters. Pharmacogenetics and Pharmacogenomics Knowledge Base. RCSB Protein Data Bank (pdb files). Ion channel web ring. Tim Hale's Cys-loop Ligand-gated Ion Channel site. Steen Pedersen (Baylor Colleg...

ase-fund.org

ASEF: American Slovenian Education Foundation

http://www.ase-fund.org/fellowship2015.html

ASEF Fellowship Program 2015. The American Slovenian Education Foundation (ASEF) fellowship program provides student financial support, allowing fellows to focus on their research. Fellowships build lasting relationships between ASEF and academic institutions. The purpose of the fellowship is to strengthen research and study exchange between Slovenia and the US with the objective of giving talented Slovenian students the ability to realize their potential to the fullest. About the ASEF fellowship. Stanfo...

proteinfoldingmachinery.net

CPFM: Center for Protein Folding Machinery

http://www.proteinfoldingmachinery.net/investigators

National Center for Macromolecular Imaging. Baylor College of Medicine. Houston, TX 77030. Dept of Biological Sciences and BioX Program. E200A James Clark Center. Stanford, CA, 94305-5430. UT MD Anderson Cancer Center. The University of Texas. MD Anderson Cancer CenterHouston. Houston, TX, 77030. William C. Mobley. Professor, Chair of Neurosciences. University of California, San Diego. 9500 Gilman Drive #0662. La Jolla, Ca 92093-0662. Senior Scientist and Professor. Building 4, Room 227. Houston, TX 77030.

proteinfoldingmachinery.com

CPFM: Center for Protein Folding Machinery

http://www.proteinfoldingmachinery.com/investigators

National Center for Macromolecular Imaging. Baylor College of Medicine. Houston, TX 77030. Dept of Biological Sciences and BioX Program. E200A James Clark Center. Stanford, CA, 94305-5430. UT MD Anderson Cancer Center. The University of Texas. MD Anderson Cancer CenterHouston. Houston, TX, 77030. William C. Mobley. Professor, Chair of Neurosciences. University of California, San Diego. 9500 Gilman Drive #0662. La Jolla, Ca 92093-0662. Senior Scientist and Professor. Building 4, Room 227. Houston, TX 77030.

proteinfoldingmachinery.org

CPFM: Center for Protein Folding Machinery

http://www.proteinfoldingmachinery.org/investigators

National Center for Macromolecular Imaging. Baylor College of Medicine. Houston, TX 77030. Dept of Biological Sciences and BioX Program. E200A James Clark Center. Stanford, CA, 94305-5430. UT MD Anderson Cancer Center. The University of Texas. MD Anderson Cancer CenterHouston. Houston, TX, 77030. William C. Mobley. Professor, Chair of Neurosciences. University of California, San Diego. 9500 Gilman Drive #0662. La Jolla, Ca 92093-0662. Senior Scientist and Professor. Building 4, Room 227. Houston, TX 77030.

benedick.rutgers.edu

Structural Biology Computational Laboratory: Software Packages

http://benedick.rutgers.edu/SBCLsoftware.html

Structural Biology Computational Laboratory. These are the software packages that are currently available on our systems. After a brief description of each program are the unix commands that run the program. The commands are case sensitive. We will add additional capabilities as necessary. InsightII (2005) and modules. Available for Academic Use. Kinemage Prekin,Reduce,Probe,Mage. Minimization methods are explained in the Forcefield-Based Simulations manual (pdf). See InsightII manual (pdf). From the Ins...

rostlab.org

People | ROSTLAB.ORG

https://www.rostlab.org/group/people

Skip to main content. Technische Universität München. Rost ( at ) .rostlab.org. Assistant. ( at ) .rostlab.org. Bernhoferm. ( at ) .rostlab.org. Juanmi. ( at ) .jmcejuela.com. Dong ( at ) .rostlab.org. Goldberg. ( at ) .rostlab.org. Hecht ( at ) .rostlab.org. Hopft ( at ) .rostlab.org. Karl ( at ) .rostlab.org. Kloppmann. ( at ) .rostlab.org. Mahlich. ( at ) .rostlab.org. Reeb ( at ) .rostlab.org. Richter. ( at ) .in.tum.de. Andrea.schafferhans. ( at ) .rostlab.org. Vicedo. ( at ) .rostlab.org. Bromberg&...

mesoscope.org

Collaborations - Mesoscope @ UCSF

http://www.mesoscope.org/collaborations

SciViz Careers and Tools. VIZBI 2013 uPy/ePMV/autoPACK Workshop. Johns Hopkins Workshop 2013. AMI ePMV workshop 2013. Behold HIV-1 0.1.6. Best Blender Animation Ever (uses ePMV too! HHMI illustration brought back to life. Immune Defense kickstarter 16 days. Johnson wins 2nd place Biophysical Society Annual Meeting 2014 Image Contest. Lecture at Faraday Discussion 169 in May, 2014. Lecture: Sampson Feldman Visiting Scholar. Ritisha Laungani receives Allan Kuchinsky Student Award. SciViz Careers and Tools.

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Andrej Sali Lab

Bull; Lab Members. Bull; Research Positions. Bull; Directions and Maps. Bull; Lab Pages. Bioinformatics, Computational Structural Biology. We are using computation grounded in the laws of physics and evolution to study the structure and function of proteins. We aim to improve and apply methods for:. Predicting the structures of proteins;. Determining the structures of macromolecular assemblies;. Annotating the functions of proteins using their structures. Congratulations to Jeremy Horst:. The paper "Stru...

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