pyrosetta.org
Documentation - PyRosetta
http://www.pyrosetta.org/documentation
Reading and Searching PyRosetta. Finding/Testing Objects and Methods. Developing and Testing New Protocols. Building PyRosetta from source. 1 Deploying PyRosetta build environment. 5 Getters and Setters. 7 Rosetta "Size" and "Real". 8 0 Indexing vs 1 Indexing. 10 Common Method Names. 11 "fullatom" vs. "centroid". A Bit of Python. A Bit of C. 1 The PyRosetta Toolkit. Making a PDB Rosetta-friendly. Hydrogen Bonds and Hydrogen Bond Scoring. Finding/Testing Objects and Methods. Help messages, produced using ".
pyrosetta.org
FAQ - PyRosetta
http://www.pyrosetta.org/faq
Please consult the forum. For additional answers or to ask a new question. 1 How do I obtain and install PyRosetta? 2 What if I have questions? 3 Is PyRosetta available for 64 bit Linux or Windows platforms? 4 How do I get started? 5 How do I cite PyRosetta? 6 What is the relationship between PyRosetta, Rosetta, and Robetta? 7 What is the relationship between The PyRosetta Toolkit GUI, PyRosetta, and PyMOL? 8 Does PyRosetta allow for parallel processing and high performance computing? 3 What objects work?
dunbrack2.fccc.edu
ProtCid:Browse:PFAM
http://dunbrack2.fccc.edu/ProtCiD/Browse/PfamsInPdb.aspx
Browse PFAM in the PDB. Click on PFAM ID to get a list of PDB entries containing the PFAM. Developed by Qifang Xu and Roland L. Dunbrack Jr; Last updated on November 25, 2015. Fox Chase Cancer Center.
dunbrack2.fccc.edu
Protein Common Interface Database
http://dunbrack2.fccc.edu/ProtCiD/PDBfam/Download.aspx
PFAM assignments in the PDB. The Pfam assignments in the entire PDB. April 11, 2016, Pfam V29.0). The PDB entities are not assigned to any PFAM. This file contains all possible sequences including those sequences with all Xs. Unassigned Unique PDB sequences. The unique PDB entities are not assigned to any PFAM, excluding those sequences with all Xs and the distinct amino acid types are less than or equal to 5. Unique means no two sequences have 100% sequence identity, and same length.
dunbrack2.fccc.edu
ProtCid:Statistics
http://dunbrack2.fccc.edu/ProtCiD/Statistics/Statistics.aspx
The database was updated on October 15, 2014. M = The number of crystal forms (CFs) that contain a common interface. Seqid = The minimum pair-wise sequence identity in a cluster. Pairs of Chain Architectures. Entries with M =2. Entries with M =2,seqid 90. Entries with M =5,seqid 90. Entries with M =10,seqid 90. Entries with M =20,seqid 90. Pairs of Chain Architectures. Clusters with M =2. Clusters with M =2,seqid 90. Clusters with M =5,seqid 90. Clusters with M =10,seqid 90. Clusters with M =20,seqid 90.
rosettacommons.org
About | RosettaCommons
https://www.rosettacommons.org/about
The hub for Rosetta modeling software. RosettaCommons makes close collaboration between laboratories the norm, even with single code modules. This allows for rapid sharing of enhancements and promotes the values of team science. RosettaCommons has a unique agreement among member universities. The source code belongs to the RosettaCommons members and is a collaborative effort among research institutions, a model that promotes shared development and discoveries. University Medical Center Schleswig-Holstein.
dunbrack2.fccc.edu
ProtCid:About
http://dunbrack2.fccc.edu/ProtCiD/About.aspx
ProtCid version 1.0 was generated at Roland Dunbrack's Lab. At Fox Chase Cancer Center. If you need any specific data that can be generated from our database, please feel free to contact the authors. Any comments, questions and suggestions, please contact the authors. Roland J. Dunbrack. Developed by Qifang Xu and Roland L. Dunbrack Jr; Last updated on November 25, 2015. Fox Chase Cancer Center.
dunbrack2.fccc.edu
ProtCid:Help
http://dunbrack2.fccc.edu/ProtCiD/Help/HelpSummary.aspx
ProtCID contains a large set of data compiled from various sources: protein structure data from the Protein Data Bank (PDB). Protein family architectures from PFAM. Biological Units from the PDB and Protein Interfaces, Surfaces and Assemblies (PISA). And alignment data generated from PISCES. And the programs FATCAT. As well as sequence information from the Universal Protein Resource (UniProt). Developed by Qifang Xu and Roland L. Dunbrack Jr; Last updated on November 25, 2015. Fox Chase Cancer Center.
dunbrack2.fccc.edu
Protein Common Interface Database
http://dunbrack2.fccc.edu/ProtCiD/PDBfam/default.aspx
Developed by Qifang Xu and Roland L. Dunbrack Jr; Last updated on November 25, 2015. Fox Chase Cancer Center.