dunbrack.fccc.edu

Home :: Dunbrack Lab

Rama(φ,ψ). Peptide ω(φ,ψ). Software for Homology Modeling of Protein Oligomers and Complexes. PDBfam: Accurate and complete Pfam assignments for the PDB. ProtCID: The Protein Common Interface Database. Nucl Acids Research, Jan 2011). PLOS Comp. Biol., Apr 2010). Conformation-dependent library for backbone geometry in proteins. Structure, Oct 2009). Virtualized webserver, webdesign: Adrian A. Canutescu and Maxim V. Shapovalov. This page was last modified on Thursday, March 22, 2018.

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Rama(φ,ψ). Peptide ω(φ,ψ). Software for Homology Modeling of Protein Oligomers and Complexes. PDBfam: Accurate and complete Pfam assignments for the PDB. ProtCID: The Protein Common Interface Database. Nucl Acids Research, Jan 2011). PLOS Comp. Biol., Apr 2010). Conformation-dependent library for backbone geometry in proteins. Structure, Oct 2009). Virtualized webserver, webdesign: Adrian A. Canutescu and Maxim V. Shapovalov. This page was last modified on Thursday, March 22, 2018.

<META> KEYWORDS

1 SCWRL

2 MolIDE

3 ArboDraw

4 protein side chain prediction

5 protein

6 proteins

7 side chain

8 prediction

9 algorithm

10 homology modeling

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people,projects,publications,software,links,libraries,rotamer,rotlibr dataset,backbone,scwrl4,bioassembmod,pisces,biodownloader,protcid/bud,arbodraw,seq2coord,news,antibody dbs,pyigclassify,pyrosetta,new bioassemblymodeler bam,powered by

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Home :: Dunbrack Lab | dunbrack.fccc.edu Reviews

https://dunbrack.fccc.edu

Rama(φ,ψ). Peptide ω(φ,ψ). Software for Homology Modeling of Protein Oligomers and Complexes. PDBfam: Accurate and complete Pfam assignments for the PDB. ProtCID: The Protein Common Interface Database. Nucl Acids Research, Jan 2011). PLOS Comp. Biol., Apr 2010). Conformation-dependent library for backbone geometry in proteins. Structure, Oct 2009). Virtualized webserver, webdesign: Adrian A. Canutescu and Maxim V. Shapovalov. This page was last modified on Thursday, March 22, 2018.

INTERNAL PAGES

dunbrack.fccc.edu

1

"Main Menu" for BioAssemblyModeler (BAM) :: Dunbrack Lab

http://dunbrack.fccc.edu/BAM

Main Menu" for BioAssemblyModeler (BAM), Release Version. Rama(φ,ψ). Peptide ω(φ,ψ). Registered BAM (also known as MolIDE2). Form for BAM License / Download here. Modeling Steps In Detail. Quick Start: Tutorial Videos. Screenshots From a Complete Homology Modeling Cycle. Image Gallery from BAM Homology modeling projects. Template of a FASTA-formatted Sequence File Serving as Input to BAM. Set of 5 Sample Sequence Files Included in BAM package. Redirects here. BAM. 20150, Release Version. BAM stands for B.

2

P20 :: Dunbrack Lab

http://dunbrack.fccc.edu/nmhrcm

Conformation-dependent library for backbone geometry in proteins. Rama(φ,ψ). Peptide ω(φ,ψ). Conformation-dependent library for backbone geometry in proteins. You can download the conformation-dependent backbone geometry library in an uncompressed, text format. Or in a zip archive. The text format is both human- and computer-friendly. The library file has Quick-Start information in its header. The publication of this work ( pdf with supplemental figures included. And its supplemental figures here.

3

NDRD :: Dunbrack Lab

http://dunbrack.fccc.edu/ndrd

Rama(φ,ψ). Peptide ω(φ,ψ). This page provides access to the neighbor-dependent Ramachandran distributions described in Ting et al., PLOS Comp. Biol. (April, 2010). This work was funded by NIH grant P20 GM76222 from the National Institutes of Health under the National Institute for General Medical Sciences, as part of the Protein Structure Initiative ( PSI2. License for the neighbor-dependent Ramachandran distributions for non-profit users: Click here. PLOS Comp. Biol. Just click and then fill out the for...

4

BioDownloader :: Dunbrack Lab

http://dunbrack.fccc.edu/BioDownloader

Rama(φ,ψ). Peptide ω(φ,ψ). Operating systems supported: Windows. Family and Mac OS. By using a Windows virtual machine). The PDB ftp server moved from ftp.rcsb.org. To ftp.wwpdb.org. And changed the PDB extension from *.ent.Z. So if you are trying to download or update PDB files, please change "Name / IP address" to ftp.wwpdb.org and "File mask" to *.ent.gz For other data files downloaded from the PDB ftp server, just update the server name. Provides the experienced user a vast set of fine-tunning option...

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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.

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dunbrack.fccc.edu

Home :: Dunbrack Lab

Rama(φ,ψ). Peptide ω(φ,ψ). Software for Homology Modeling of Protein Oligomers and Complexes. PDBfam: Accurate and complete Pfam assignments for the PDB. ProtCID: The Protein Common Interface Database. Nucl Acids Research, Jan 2011). PLOS Comp. Biol., Apr 2010). Conformation-dependent library for backbone geometry in proteins. Structure, Oct 2009). Virtualized webserver, webdesign: Adrian A. Canutescu and Maxim V. Shapovalov. This page was last modified on Thursday, March 22, 2018.

dunbrack.org

Dunbrack Genealogy

Welcome to the Dunbrack Family Genealogy Page. The roots of the Dunbrack family are in Aberdeenshire. The first person with the Scottish surname Dumbreck. Was Philip de Dumbreck, who was born about 1320, and was the first Sheriff-Depute of Aberdeenshire in the 1340s and 1350s. Dumbreck is a set of farms about 15 miles north of Aberdeen:. The name is probably derived from the Gaelic, Druim breac. Which means "spotted ridge." In the early sources, the name is often spelled Drumbreck or Drumbrek. Dating fro...

dunbrack2.fccc.edu

Protein Common Interface Database

PFAM assignments in the PDB improved by consensus sequences, HMM-HMM alignmnets, and structure alignments. Protein Common Interfaces Database. Based on Pfam v31.0 and the PDB of June 2017). ProtCID now contains clusters of Pfam domain interfaces, Pfam-peptide interfaces and Pfam-DNA/RNA/Ligands interactions. For domain-domain interfaces, we use Pfam domains defined in our PDBfam database. PDB entries are grouped into Pfam-Pfam relations. One entry may belong to different Pfam-Pfam relations, if i...Pfam-...

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Dunbrack Family

Whats happening with us. Wednesday, July 14, 2010. Uncle Brian and Isaac. Can't wait till our next visit. we miss you Uncle Brian! Wednesday, July 14, 2010. Thursday, July 1, 2010. Elise's Birthday. On her actual day. Happy 3rd Birthday my princess. You mean the world to us. we love you very much. Sorry the pics are in the reverse order. Elise checking out her new gift from Mommy, Daddy and Isaac. Checking out the gifts from Grandma and Papa. Papa giving Elise a birthday hug. I can't believe she is 3!

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