SlideFinderPowerPoint search engine with thumbnail results
Advanced search
Newest Viewed Downloaded

Universities > United States Showing 1 - 20 of 62 items

Dowling College

Dowling College is an accredited private college with its main campuses at Oakdale, Shirley and Melville in Suffolk County, New York, with more than 6,500 full-time and part-time undergraduate and graduate students through four schools: the School of Arts & Sciences, Townsend School of Business, School of Education and School of Aviation. Dowling's most recognized programs are in Aviation Management, Education, and Computer Science.

More information: http://en.wikipedia.org/wiki/Dowling_College

Protein-Protein Interaction in the Rho-RhoGAP Complex Eno Akpovwa, Paul Craig, Herbert Bernstein, Rochester Institute of Technology, Rochester, NY and Dowling College, Oakdale, NY. Abstract The RhoGAP (Rho GTPase Activating Protein) family of proteins regulates G-protein signal transduction cascades by increasing the slow intrinsic GTP to GDP hydrolysis by Rho. The Rho family of small G proteins tranduces signals from plasma-membrane receptors and controls cell adhesion, motility and shape by actin cytoskeleton formation. This process occurs through transient protein-protein interactions between RhoGAP and its targets, Rho, Cdc42 and Rac. Rho and its homologs interact with RhoGAP by packing together with the RhoGAP protein, so that their switch I and II regions slot into a shallow pocket on RhoGAP, making polar and non-polar interactions with RhoGAP. Using a molecular graphics program (PyMol) with a plug-in designed at RIT (ProMol); the small structural motifs involved in the Rho-RhoGAP interaction have been explored. Two RhoGAP motifs were created – one was based on conserved residues involved in protein-protein interactions and the second was based on five residues that promote GTP hydrolysis. These motifs were then tested using a series of RhoGAP homologs. The results demonstrated that the Motif Maker tool in ProMOL is able to discriminate between RhoGAP homologs that actively target Rho and those homologs that share fold similarity with RhoGAP, but are not able to int...

RasMol to PyMOL Scripting Language Conversions Scott Mottarella, Brett Hanson, Charles Westin, Paul Craig, Herbert Bernstein, Rochester Institute of Technology, Rochester, NY, and Dowling College, Oakdale, NY. Abstract (W0085-5121) The aim of the Structural Biology Extensible Visualization Structure Language project is to develop a tool that allows the use of multiple molecular visualization programs without requiring the user to learn a new scripting language. ConSCRIPT is the first such tool. There are many software programs available ranging from the difficult to understand yet mathematically versatile and graphically stunning PyMOL to the user-friendly and familiar RasMol. Each program comes with its own scripting language essential to its functionality. Coordination between these programs is often necessary across projects and sometimes even among them. Valuable time can be lost learning a new visualization program and its scripting language. ConSCRIPT, as the first such iteration of the SBEVSL project, is a plug-in for PyMOL that understands commands entered in the RasMol scripting language as either a premade script or singly from PyMOL’s own command line. Future work will include other molecular visualization programs including scripting into RasMol, Jmol and Chime. ConScript is can be downloaded from the SBEVSL Sourceforge site, https://sourceforge.net/projects/sbevsl/. The project is funded in part by NIGMS grant #1R15GM078077. Map Support for RasMol map command...
A simplified scripting language which can easily translate to the three established molecular graphics scripting languages, Pymol, Rasmol, and Jmol

A simplified scripting language which can easily translate to the three established molecular graphics scripting languages, Pymol, Rasmol, and Jmol
A Pair-Based Approach to Structural Homology Using Quaternion SLERP Averaging and Local Rotations Lawrence C. Andrews* and Herbert J. Bernstein#

A Pair-Based Approach to Structural Homology Using Quaternion SLERP Averaging and Local Rotations Lawrence C. Andrews* and Herbert J. Bernstein#

* * Andrews, Bernstein: Local Rotations
CIFFOLD Managing Long Lines in CIF by Kostadin Mitev, Georgi Todorov, Herbert J. Bernstein Department of Mathematics and Computer Science Dowling College, Oakdale, NY 11769 USA Work funded in part by a grant from the IUCr

CIFFOLD Managing Long Lines in CIF by Kostadin Mitev, Georgi Todorov, Herbert J. Bernstein Department of Mathematics and Computer Science Dowling College, Oakdale, NY 11769 USA Work funded in part by a grant from the IUCr

Using RasMol, PyMOL and Jmol with the Structural Biology Extensible Visualization Scripting Language (SBEVSL) P. A. Craig*, S. E. Mottarella*, C. Wischmeyer*, H. J. Bernstein^, I. Awuah Asiamah, D. Boycheva^, G. Darakev^, N. Darakev^, P. Gozo^, J. Jemilawon^, N. Jia^, P. Kamburov^, G. McQuillan^, D. O'Brien^, G. Todorov^ *Rochester Institute of Technology, Rochester NY 14623, ^Dowling College, Oakdale, NY 11769 Abstract W0073 There are many useful molecular graphics programs, but moving among them can be challenging. The Structural Biology Extensible Visualization Scripting Language (SBEVSL) project is working to simplify the task of starting a graphics presentation under one package, e.g. RasMol or Jmol and then moving to another package, such a PyMOL or CCP4mg for, say, better renderings of certain features without having to redo all the work of selecting orientations and types of displays. For some uses, the scripting language can be used a block box, much the way we use Postscript for text documents, but, where feasible, SBEVSL is designed to be comprehensible to scientists by using simple menu-click-like commands and reasonable defaults. RasMol, PyMOL and Jmol are being given "native“ SBEVSL support and external translators will allow the approach to be applied with other packages, such as CCP4mg. This work is part of the combined efforts of the SBEVSL groups at Dowling College and Rochester Institute of Technology.. Work supported in part by grant 1R15GM078077-01 fro...

W0049 For many educators and scientists, PyMOL is the application of choice for preparing images and animations of their structures because of the beauty and quality of the images. However, many are most familiar with the scripting languages associated with RasMol, Chime and Jmol. The long-range goal of our Structural Biology Extensible Visualization Scripting Language project is to make the multiple molecular visualization tools available to the broadest possible audience, where each user can use many programs, with knowledge of the scripting language for only one of those programs. The first step has been a comparison of the command sets for RasMol and PyMOL, followed by creation of a plug-in for PyMOL that will accept RasMol script files, translate the commands into PyMOL script and execute the commands. The process involves searching for recognized, valid, RasMol script commands and performing its PyMOL equivalent, either as a single command or as a series of commands that produce the same result. Future plans include expansion to additional molecular visualization programs and the preparation of a web site to provide script translation among the various programs. The project is funded in part by NIGMS grant #1R15GM078077. cmd.load( "C:\Documents and Settings\Scotthew. KYLE\Desktop\\1D66.pdb" ) cmd.rotate( 'x', 180 ) cmd.select( 'resn asp+glu+arg+lys+his+asn+thr+ cys+gln+tyr+ser+gly+ala+leu+val+ile+ met+tr...
SBEVSL Structural Biology Extensible Visualization Scripting Language PyMOL to and from SBEVSL

SBEVSL Structural Biology Extensible Visualization Scripting Language PyMOL to and from SBEVSL

Abstract: Structural biologists and molecular scientists in many other disciplines need to communicate effectively about biological macromolecules. The number and complexity of available structures are both increasingly dramatically. There are many free molecular visualization programs that facilitate macromolecular structure analysis and experimental design. Each program has distinct features and limitations, often leading researchers to utilize multiple programs to successfully investigate all qualities of macromolecular structure. To alleviate this problem, we are creating a common ontology called the Structural Biology Extensible Visualization Scripting Language (SBEVSL) that will serve as a central resource for communicating scripts between different visualization programs. As a first step, we have prepared a list of individual commands that are used in PyMOL, as well as groups of commands which we are calling “features” to serve as input to SBEVSL. We have also created a plug-in for PyMOL that can take information from the central ontology by reading files line by line, find the associated commands, and output them to another script file. Future steps will script interchange between PyMOL, Rasmol, Jmol and Chime using the SBEVSL ontology as the intermediary in the communication. The completion of this project will allow researchers to move easily between these programs and quickly reproduce the same view in each program, giving them more time to spend on analysi...
ProMOL: Simplification and Increased Functionality of PyMOL By Brett Hanson, Charlie Westin, Paul Craig, and Len Slatest

ProMOL: Simplification and Increased Functionality of PyMOL By Brett Hanson, Charlie Westin, Paul Craig, and Len Slatest
SBEVSL Structural Biology Extensible Visualization Scripting Language PyMOL to and from SBEVSL

SBEVSL Structural Biology Extensible Visualization Scripting Language PyMOL to and from SBEVSL

Abstract: Structural biologists and molecular scientists in many other disciplines need to communicate effectively about biological macromolecules. The number and complexity of available structures are both increasingly dramatically. There are many free molecular visualization programs that facilitate macromolecular structure analysis and experimental design. Each program has distinct features and limitations, often leading researchers to utilize multiple programs to successfully investigate all qualities of macromolecular structure. To alleviate this problem, we are creating a common ontology called the Structural Biology Extensible Visualization Scripting Language (SBEVSL) that will serve as a central resource for communicating scripts between different visualization programs. As a first step, we have prepared a list of individual commands that are used in PyMOL, as well as groups of commands which we are calling “features” to serve as input to SBEVSL. We have also created a plug-in for PyMOL that can take information from the central ontology by reading files line by line, find the associated commands, and output them to another script file. Future steps will script interchange between PyMOL, Rasmol, Jmol and Chime using the SBEVSL ontology as the intermediary in the communication. The completion of this project will allow researchers to move easily between these programs and quickly reproduce the same view in each program, giving them more time to spend on analysi...
ProMOL: Simplification and Increased Functionality of PyMOL By Brett Hanson, Charlie Westin, Paul Craig, and Len Slatest

ProMOL: Simplification and Increased Functionality of PyMOL By Brett Hanson, Charlie Westin, Paul Craig, and Len Slatest
Universal Linear Algebra API based on M4 Michael Fiero Isaac Asiamah

Universal Linear Algebra API based on M4 Michael Fiero Isaac Asiamah
Advanced Formatting Techniques Advanced Ami Pro for OS/2

Advanced Formatting Techniques Advanced Ami Pro for OS/2
Economic Trade Analysis Tool Michael Fiero Isaac Asiamah Jonathan Ihm

Economic Trade Analysis Tool Michael Fiero Isaac Asiamah Jonathan Ihm
Economic Trade Analysis Tool Input/Output Isaac Asiamah Michael Fiero Jonathan Ihm

Economic Trade Analysis Tool Input/Output Isaac Asiamah Michael Fiero Jonathan Ihm
Microsoft Word 2000 ADVANCED LEVEL

Microsoft Word 2000 ADVANCED LEVEL

Macromedia Director 8 Advanced Level Course

Macromedia Director 8 Advanced Level Course
Protein-Protein Interactions in the Multi-enzyme Pyruvate Dehydrogenase Complex Presented by: Katrina L. Henry Paul Craig†*, Herbert J. Bernstein‡* †RIT, Department of Chemistry, Molecular Visualization Lab Katrina Henry kleehenry@gmail.com ‡Dowling College, Department of Mathematics and Computer Science (347) 469-5734 140 Carver Loop Bronx, NY 10475

Protein-Protein Interactions in the Multi-enzyme Pyruvate Dehydrogenase Complex Presented by: Katrina L. Henry Paul Craig†*, Herbert J. Bernstein‡* †RIT, Department of Chemistry, Molecular Visualization Lab Katrina Henry kleehenry@gmail.com ‡Dowling College, Department of Mathematics and Computer Science (347) 469-5734 140 Carver Loop Bronx, NY 10475

Abstract Proteins, throughout their lifetime, interact with multiple protein partners. The functions of a protein may depend mainly on these protein-protein interactions. In the case of the multi-subunit pyruvate dehydrogenase complex, these interactions help form a protein complex that is stable throughout the functional life of the protein. The complex consists of three different protein components, E1, E2, and E3. The E3 component, known as dihydrolipoyl dehydrogenase, is bound to an E2 inner core by a binding domain, also referred to as E3BD, PSBD, E2BD, or E3BP (BD – binding domain/ BP – binding protein). The binding domain is a very small conserved protein structure. The E3 component “docks”, or attaches to the binding domain using a small number of conserved amino acid residues, both on the E3 component itself and on the binding domain, which vary, to some extent, between gram (+) bacteria, gram (-) bacteria, and mammalian species. Together, E3 and the binding domain form an electrostatic zipper of charge-charge interactions, ensuring that the components are fairly tightly bound. Small structural motifs of the electrostatic zipper in the different species were created using the ProMOL plug-in for the PyMOL molecular graphics environment. The electrostatic zipper motifs were then compared among several species; the utility of the motifs created with ProMOL in defining, comparing and distinguishing small structural motifs will be presented. ...
1234 Next >>
Sitemap