polyview.cchmc.org
POLYVIEW-2D protein structure visualization serverPOLYVIEW-2D generates images with protein structure / function annotation in the form of sequence profiles.
http://polyview.cchmc.org/
POLYVIEW-2D generates images with protein structure / function annotation in the form of sequence profiles.
http://polyview.cchmc.org/
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POLYVIEW-2D protein structure visualization server | polyview.cchmc.org Reviews
https://polyview.cchmc.org
POLYVIEW-2D generates images with protein structure / function annotation in the form of sequence profiles.
polyview.cchmc.org
POLYVIEW: Image Gallery
http://polyview.cchmc.org/gallery.html
To submit an image to the gallery, first generate it using POLYVIEW-2D/3D/MM and then follow the link provided next to the image. Link is valid for two weeks only since the image creation. Multiple submissions using the same link will update the image annotation only.
POLYVIEW - 3D (Submission Form)
http://polyview.cchmc.org/polyview3d.html
Versatile annotation and high quality visualization. Source of Structural Data ( Help. Examples: 3ert, 1ttu, 1naq. Get ID by keyword. Upload custom structure in the PDB format. For files containing additional annotations, such as those generated using, e.g., SPPIDER, ConSurf, or MolMovDB, specify the file/annotation type in the Structure annotation. Overall Structure View ( Help. Or superimpose all models. Or specify it manually:. Eg A:150 or B: or :30). Chain Color and Rendering ( Help. All in same color.
POLYVIEW-2D: Documentation
http://polyview.cchmc.org/polyview_doc.html
Terms of use and disclaimer. References to cite the server. Review of protein structure prediction. Analysis of protein complexes. Review of amino acid conservation. Automated annotations using scripts. Pictorial definitions used in POLYVIEW-2D for protein representation. Amino acid residue numeration. H - α and other helices (view 1). H - α and other helices (view 2). E - β-strand or bridge. Relative solvent accessibility (RSA). 0 - completely buried (0-9% RSA),. 9 - fully exposed (90-100% RSA). The POL...
POLYVIEW-MM - Explorer of molecular motions
http://polyview.cchmc.org/conform.html
Analysis and visualization of the ensembles of molecular models. Structural Data in 3D Coordinates ( Help. Get ID by keyword. Molecular structure in a custom coordinate file. Pdb (Protein Data Bank). 50 MB file size limit). Expected formats: NAMD and CHARMM=dcd/psf GROMACS=trr/gro). Type of conformational analysis. Ensemble of NMR models. Examples: 2kmv, 2kcj). Morph or low-frequency motion. MD or other trajectory. Examples: 1lo1, 2jpa). E-mail address ( optional.
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AP eLab - Methodological Projects
http://aplab.cchmc.org/projects_method.html
E-Laboratory of Aleksey Porollo. These 1D predictions are often the first step to gaining insight into the 3D structure and function of a protein. Accurate prediction of relative solvent accessibilities of amino acid residues in proteins may be used to facilitate protein structure prediction and functional annotation. Toward that goal, we have developed a novel method (SABLE) for improved prediction of relative solvent accessibilities (RSA) ( Ref 1. Trans-membrane domains ( Ref 3. Adamczak R, Porollo A, ...
User Testimonials | Research IT Core Services
https://bmi.cchmc.org/resources/user-testimonials
Installing OpenNX in Mac OS X Lion. Running software the easy way. Mac, Linux and Solaris Support. Biomaterial Tracking and Management (BTM) Core. SNPGWA, and Haploview) installed and running on the cluster. Our specific requirements have presented challenges along the way, and the BMI staff has been extremely responsive to our needs. Without the hardware and personnel support from BMI, our research would be much more difficult. Michael Barnes, PhD. Todd Nick, PhD. Ge Zhang, PhD. Douglas Kojetin, PhD.
Web tools and servers
https://folding.cchmc.org/software/software.html
Public domain software available for downloading . Program for accurate prediction of real-valued relative solvent accessibility (RSA) and secondary structures of amino acid residues in proteins. This is a stand-alone version of the SABLE. Sable v. 1.0 ( SABLE 1. PC distribution (includes source code, ready to be compiled under Cygwin). DOWNLOAD. Sable v. 2.0 ( SABLE 2. For details). DOWNLOAD. Sift v. 1.0: Unix distribution (includes source code, easy to port to other platforms). DOWNLOAD. Program for pr...
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POLYVIEW-2D protein structure visualization server
Protein structure annotation using sequence profiles. Structural Data in 3D Coordinates ( Help. Examples: 3ert, 1ttu, 1naq. Get ID by keyword. Custom structure in the PDB format. Given coordinate file represents a multi-model structure,. Such as NMR (e.g., PDB ID 2kmv, 2kcj), morph ( example. Or low-frequency motion ( example. Structural Data from Predictions ( Help. Reference number from the link given in the SABLE email ( following the FName. File with the saved SABLE email message. AND at least one.
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HOME – Polyvig
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