biomachina.org

biomachina.org

Old version of this site. Wahle and Wriggers. "Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor" PLOS Computational Biology, 2015. Wriggers and He. "Numerical geometry of map and model assessment" J. Struct Biol. 2015. We have recently moved. Our lab has moved to Old Dominion University in Norfolk, Virginia. Our current personnel includes:. Willy Wriggers, Ph.D. (Professor, MAE). Julio Kovacs, Ph.D. (Senior Staff Scientist).

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Old version of this site. Wahle and Wriggers. Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor PLOS Computational Biology, 2015. Wriggers and He. Numerical geometry of map and model assessment J. Struct Biol. 2015. We have recently moved. Our lab has moved to Old Dominion University in Norfolk, Virginia. Our current personnel includes:. Willy Wriggers, Ph.D. (Professor, MAE). Julio Kovacs, Ph.D. (Senior Staff Scientist).

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biomachina.org | biomachina.org Reviews

https://biomachina.org

Old version of this site. Wahle and Wriggers. "Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor" PLOS Computational Biology, 2015. Wriggers and He. "Numerical geometry of map and model assessment" J. Struct Biol. 2015. We have recently moved. Our lab has moved to Old Dominion University in Norfolk, Virginia. Our current personnel includes:. Willy Wriggers, Ph.D. (Professor, MAE). Julio Kovacs, Ph.D. (Senior Staff Scientist).

SUBDOMAINS

modehunter.biomachina.org

Other Sites of Interest:. Is a Python-based program package for the normal mode analysis of coarse grained elastic networks. The package includes the classic elastic network algorithm, the new bend-twist-stretch algorithm for arbitrary coarse networks, and various useful tools for analysis and animation of modes. Please send any inquiries, bug reports, etc. to modehunter at biomachina.org.

emotion.biomachina.org

Is a database for animations of electron microscopy maps generated from physics-based deformable models. em. Was originally developed by biomachina. Member Essam Metwally, Ph.D., at The Scripps Research Institute. Enter Search Criteria* :. Currently Queries are restricted to EMotion Protein ID Sequences. Pattern Matching is conducted on the entire ID Sequence. Enter a blank query to retrieve a complete listing of our holdings. June 29, 2007. October 8, 2002. Click on the map you would like to view.

birmanns.biomachina.org

biomachina.org

Old version of this site. Wahle and Wriggers. "Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor" PLOS Computational Biology, 2015. Wriggers and He. "Numerical geometry of map and model assessment" J. Struct Biol. 2015. We have recently moved. Our lab has moved to Old Dominion University in Norfolk, Virginia. Our current personnel includes:. Willy Wriggers, Ph.D. (Professor, MAE). Julio Kovacs, Ph.D. (Senior Staff Scientist).

timescapes.biomachina.org

Other Sites of Interest:. Python tools for normal mode analysis. D E Shaw Research. And is available without cost for both non-commercial and commercial use. Please send any inquiries, bug reports, etc. to timescapes at biomachina.org.

wriggers.biomachina.org

biomachina.org

Old version of this site. Our lab has moved to Old Dominion University in Norfolk, Virginia. Our current personnel includes:. Willy Wriggers, Ph.D. (Professor, MAE). John Heumann, Ph.D. (Consultant). Donald Lear (Graduate Student, MAE). Andrew Hinton (Graduate Student, MSVE). Dara Emami (Undergraduate Student, MAE). Stephen Buchanan (Undergraduate Student, MAE).

situs.biomachina.org

Download v. 2.7.2. NYSBC Course, New York. EMBO Course 09, Grenoble. Innovations 06", Houston. Situs Workshop 03, San Diego. Other Sites of Interest:. Our lab has moved to Old Dominion University in Norfolk, Virginia. Situs now an SBGrid supported application. Describes many of the Situs conventions (such as correlation, resolution, map formats) and scripting enabled work flows. Utility for detecting filamentous densities (such as alpha-helices and actin filaments) ( Rusu and Wriggers, 2012. Program pack...

sensitus.biomachina.org

biomachina.org

Old version of this site. Our lab has moved to Old Dominion University in Norfolk, Virginia. Our current personnel includes:. Willy Wriggers, Ph.D. (Professor, MAE). John Heumann, Ph.D. (Consultant). Donald Lear (Graduate Student, MAE). Andrew Hinton (Graduate Student, MSVE). Dara Emami (Undergraduate Student, MAE). Stephen Buchanan (Undergraduate Student, MAE).

sculptor.biomachina.org

Sculptor

Sculptor is an interactive multi-resolution docking and visualization program for low-resolution density maps and atomic structures. We are developing Sculptor as a GUI-based extension of the Situs docking programs, to allow an interactive exploration and analysis of volumetric maps. Sculptor combines 3D rendering with advanced mathematical concepts like clustering techniques and pattern matching algorithms to permit an almost instantaneous fitting of the high-resolution structures and to facilit...And s...

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biomachina.org

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biomachina.org - old version

http://www.biomachina.org/index_old.html

We are moving and we are hiring! Biomachina.org found a new home at Old Dominion University in Norfolk, Virginia. Will be the Frank Batten Professor of Mechanical and Aerospace Engineering. ODU has a long tradition in government and industrial applications of 3D modeling and visualization. We will complement the growing number of computational life sciences and biomedical engineering programs on campus. Popular multi-scale docking and modeling suite developed since 1998.

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situs.biomachina.org

Innovations 2006 Houston

http://situs.biomachina.org/hn06

Innovations in Nanoscale Modeling and Imaging of Biological Systems. Organized a training workshop. April 17-23, 2006, in Houston, Texas. The major goal of this workshop was to train participants from the fields of electron microscopy and x-ray diffraction in the use of our modeling, imaging, and visualization software with an emphasis on interfaces with compatible software used in the structural biology community. A secondary goal was to foster an alliance with innovative leaders.

situs.biomachina.org

SAXS Docking

http://situs.biomachina.org/saxs/index.html

Thanks for your interest. Please select any of the following links:. Supplementary figures and data. For the manuscript Using Situs. For the registration of protein structures with low-resolution bead models from X-Ray solution scattering. By W Wriggers and P. Chacón, J. Appl. Cryst. 34:773-776, 2001. Main page and download).

sculptor.biomachina.org

Download Sculptor

http://sculptor.biomachina.org/download.html?option=com_content&view=article&id=54&Itemid=68

Sculptor is available for free, but to download the software please register first following the steps below. The information given will only be used to alert you of any new releases or to count the number of users. Sculptor is available in easy to install packages for Windows (setup.exe), Mac OS X (dmg packages for Intel Macs) and Linux (tgz packages for 32 and 64Bit kernels after 2006), and as source code. Please click here to start the download process.

sculptor.biomachina.org

Tutorials

http://sculptor.biomachina.org/tutorials.html?option=com_content&view=category&id=37&Itemid=71

Our tutorials focus on specific tasks that can be accomplished with Sculptor. If you are interested in a user guide you can download the PDF guide. Or consult the online Documentation. If you still cannot find an answer to a question, please contact us by e-mail under sculptor at biomachina.org. Now select one of the workflow tutorials:. Tutorial - Visualization of Molecular Structures. Tutorial - Visualization of Volumetric Data. Tutorial - Feature-Based Docking. Tutorial - Feature-Based Flexible Fitting.

sculptor.biomachina.org

Tutorial - Feature-Based Flexible Fitting

http://sculptor.biomachina.org/tut.flexing.html?option=com_content&view=article&id=63

Tutorial - Feature-Based Flexible Fitting. This tutorial describes how to use Sculptor to perform the feature-based flexible fitting of multi-resolution data sets. The high-resolution atomic structure and low-resolution volumetric map of the RNA Polymerase (Darst. PNAS, 2002) are provided and will be utilized to demonstrate the flexible fitting by interpolation method. Data Flow and Design. The multi-resolution data set of RNA Polymerase provide here was already aligned. To cartoon (select "rnap.pdb"...

sculptor.biomachina.org

Sculptor

http://sculptor.biomachina.org/index.html

Recent releases have added routines to efficiently model conformational differences, to interactively carry out the peak-selection for exhaustive search tools, and have added accelerated visualization techniques using programmable-GPUs. Sculptor Version 2.1. The latest release of Sculptor includes the new multi-scale ambient occlusion illumination ( Wahle and Wriggers, 2015. Starosolski et al., 2012. Rusu and Wriggers, 2012. Rusu et al., 2012. 64bit Linux ( 2006 and later). 32bit Linux ( 2006 and later).

sculptor.biomachina.org

Documentation

http://sculptor.biomachina.org/documentation.html?option=com_content&view=category&id=36&Itemid=60

You can find an extensive user guide in PDF format, including a description of the Lua scripting language, here:. Click to download the Sculptor 2 user guide in PDF format. Alternatively, the following simplified graphical documentation is organized around certain topics, like the user interface or the visualization of certain document types. It also provides a short description of every menu-item. If you still cannot find an answer to a question, please also check the Tutorials. User Manual - File Menu.

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Old version of this site. Wahle and Wriggers. "Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor" PLOS Computational Biology, 2015. Wriggers and He. "Numerical geometry of map and model assessment" J. Struct Biol. 2015. We have recently moved. Our lab has moved to Old Dominion University in Norfolk, Virginia. Our current personnel includes:. Willy Wriggers, Ph.D. (Professor, MAE). Julio Kovacs, Ph.D. (Senior Staff Scientist).

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