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DBAli tools: mining the protein structure space

M. A. Marti-Renom, U. Pieper, M. S. Madhusudhan, A. Rossi, N. Eswar, F. P. Davis, F. Al-Shahrour, J. Dopazo, A. Sali
2007 Nucleic Acids Research  
The DBAli tools use a comprehensive set of structural alignments in the DBAli database to leverage the structural information deposited in the Protein Data Bank (PDB).  ...  that identifies domains as recurrent structural fragments and (v) an implementation of the COMPARER method in the SALIGN command in MODELLER that creates a multiple structure alignment for a set of related  ...  The DBAli database The DBAli database contains pairwise and multiple structure alignments of protein structures in the PDB.  ... 
doi:10.1093/nar/gkm236 pmid:17478513 pmcid:PMC1933139 fatcat:uimvsv7rgrajlczypwgi6jfnyy

MODBASE: a database of annotated comparative protein structure models and associated resources

U. Pieper
2006 Nucleic Acids Research  
Our other resources integrated with MODBASE include comprehensive databases of multiple protein structure alignments (DBAli, http://salilab.org/dbali), structurally defined ligand binding sites and structurally  ...  MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure.  ...  For linking to MODBASE from their databases, we thank David Haussler, Jim Kent (UCSC Genome Browser), Amos Bairoch (SwissProt/TrEMBL), Rolf Apweiler (InterPro), Patsy Babbitt (SFLD), and Kathy Wu (PIR/  ... 
doi:10.1093/nar/gkj059 pmid:16381869 pmcid:PMC1347422 fatcat:quimgf3kibesrcsogatfoeizp4

ModBase, a database of annotated comparative protein structure models and associated resources

Ursula Pieper, Benjamin M. Webb, Guang Qiang Dong, Dina Schneidman-Duhovny, Hao Fan, Seung Joong Kim, Natalia Khuri, Yannick G. Spill, Patrick Weinkam, Michal Hammel, John A. Tainer, Michael Nilges (+1 others)
2013 Nucleic Acids Research  
MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models.  ...  MODBASE currently contains 5 152 695 reliable models for domains in 1 593 209 unique protein sequences; only models based on statistically significant alignments and/or models assessed to have the correct  ...  ACKNOWLEDGEMENTS We are grateful to Tom Ferrin, Daniel Greenblatt, Conrad Huang and Tom Goddard for CHIMERA and For linking to MODBASE from their databases, we thank Torsten Schwede (Protein Model Portal  ... 
doi:10.1093/nar/gkt1144 pmid:24271400 pmcid:PMC3965011 fatcat:qjyw5cf25ndxpmlts7drmoc5ku

Structure Comparison and Alignment [chapter]

Philip E. Bourne, Ilya N. Shindyalov
2005 Methods of biochemical analysis  
As of August 2007, the DBAli database contained $1.67 billion pair-wise structure alignments calculated by MAMMOTH.  ...  Finally, the SALIGN command of the MODELLER package , which is also used in the DBAli database, compares structure properties calculated from the 3D coordinates of two or more proteins that are then aligned  ... 
doi:10.1002/0471721204.ch16 fatcat:rehizpnzsbbjfgi7jjef6slssm

ModView, visualization of multiple protein sequences and structures

V. A. Ilyin, U. Pieper, A. C. Stuart, M. A. Marti-Renom, L. McMahan, A. Sali
2003 Bioinformatics  
ModView integrates a multiple structure viewer, a multiple sequence alignment editor, and a database querying engine.  ...  We describe ModView, a web application for visualization of multiple protein sequences and structures.  ...  The project has been supported partly by a grant from NIH (P50-GM62529).  ... 
doi:10.1093/bioinformatics/19.1.165 pmid:12499313 fatcat:pjfg4fcnlnh7lm43dvbythfrpu

Tools for comparative protein structure modeling and analysis

N. Eswar
2003 Nucleic Acids Research  
of MODWEB for building comparative models based on distant known structures; MODBASE, a comprehensive database of annotated comparative models for all sequences detectably related to a known structure  ...  The following resources for comparative protein structure modeling and analysis are described (http://salilab.org): MODELLER, a program for comparative modeling by satisfaction of spatial restraints; MODWEB  ...  Fourthly, improvement of the modeling techniques is served by DBALI, a comprehensive database of multiple protein structure alignments calculated by the SALIGN command of MODELLER (38) and the EVA-CM  ... 
doi:10.1093/nar/gkg543 pmid:12824331 pmcid:PMC168950 fatcat:7h4x7vmc7rbh7nzath35dod2x4

IMPROVING HOMOLOGY MODELS FOR PROTEIN-LIGAND BINDING SITES

Chris Kauffman, Huzefa Rangwala, George Karypis
2008 Computational Systems Bioinformatics  
In order to improve the prediction of protein-ligand binding sites through homology modeling, we incorporate knowledge of the binding residues into the modeling framework.  ...  Binding labels are used with a very sensitive sequence alignment method to align the target and template. Relevant parameters governing the alignment process are searched for optimal values.  ...  These include the MODELLER modified residue table, the cross-validation results of section 5.2.5 and the binary programs for extraction, sequence alignment, and structure alignment.  ... 
doi:10.1142/9781848162648_0019 fatcat:w5piorowwffqphmmnofennitzm

ModBase, a database of annotated comparative protein structure models, and associated resources

U. Pieper, B. M. Webb, D. T. Barkan, D. Schneidman-Duhovny, A. Schlessinger, H. Braberg, Z. Yang, E. C. Meng, E. F. Pettersen, C. C. Huang, R. S. Datta, P. Sampathkumar (+5 others)
2010 Nucleic Acids Research  
ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models.  ...  The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org  ...  (http://salilab.org/pibase) (24) , the DBAli database of structural alignments (http://salilab.org/ dbali) (25, 26) and the LS-SNP database of structural annotations of human non-synonymous single-nucleotide  ... 
doi:10.1093/nar/gkq1091 pmid:21097780 pmcid:PMC3013688 fatcat:kmqbpcx7sfek7jxgh4mmv2vley

MODBASE, a database of annotated comparative protein structure models, and associated resources

U. Pieper
2004 Nucleic Acids Research  
ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models.  ...  The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkh095 pmid:14681398 pmcid:PMC308829 fatcat:blq5hwxzh5gobc32e6c5y3gu6a

The Structure of Chagasin in Complex with a Cysteine Protease Clarifies the Binding Mode and Evolution of an Inhibitor Family

Stephanie X. Wang, Kailash C. Pandey, Julio Scharfstein, James Whisstock, Rick K. Huang, Jordan Jacobelli, Robert J. Fletterick, Philip J. Rosenthal, Magnus Abrahamson, Linda S. Brinen, Andrea Rossi, Andrej Sali (+1 others)
2007 Structure  
Protein inhibitors of cysteine proteases may have evolved more than once on nonhomologous scaffolds. Structure 15, 535-543,  ...  We report the 2.2 Å crystal structure of the signature member of the I42 family, chagasin, in complex with a cysteine protease.  ...  S.X.W. was a recipient of a postdoctoral fellowship from the American Heart Association. Received: November 21, 2006 Revised: March 1, 2007 Accepted: March 20, 2007 Published: May 15, 2007  ... 
doi:10.1016/j.str.2007.03.012 pmid:17502099 fatcat:hkiyg2be6zbpjgwq3uravxqmkm

MODBASE, a database of annotated comparative protein structure models and associated resources

U. Pieper, N. Eswar, B. M. Webb, D. Eramian, L. Kelly, D. T. Barkan, H. Carter, P. Mankoo, R. Karchin, M. A. Marti-Renom, F. P. Davis, A. Sali
2009 Nucleic Acids Research  
ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models.  ...  The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkn791 pmid:18948282 pmcid:PMC2686492 fatcat:uy2vgrqqljfuhozumatnojgolu

The 2006 Automated Function Prediction Meeting

Ana PC Rodrigues, Barry J Grant, Adam Godzik, Iddo Friedberg
2007 BMC Bioinformatics  
The California Institute for Telecommunication and Information Technology (CalIT2) provided AFP 2006 with conference space, a hall, logistic and technical support.  ...  John Wooley, Associate Vice Chancellor for Research at the University of California San Diego, whose generous invitation to the campus of the University of California at San Diego secured this meeting's  ...  Marti-Renom and colleagues [12] introduce two new programs, AnnoLite and AnnoLyze, which add functional content to the previously established DBAli database of protein structure alignments [13] .  ... 
doi:10.1186/1471-2105-8-s4-s1 pmid:17570143 pmcid:PMC1892079 fatcat:4g2fezgshzbcxb7ez5aixla2fi

Comparative Modeling of Drug Target Proteins☆ [chapter]

B. Webb, N. Eswar, H. Fan, N. Khuri, U. Pieper, G.Q. Dong, A. Sali
2014 Reference Module in Chemistry, Molecular Sciences and Chemical Engineering  
Other resources associated with ModBase include a comprehensive database of multiple protein structure alignments (DBALI), 281 structurally defined ligand-binding sites, 319 structurally defined binary  ...  /repository/ Miscellaneous DBALI 281 http://www.salilab.org/dbali GENECENSUS 282 http://bioinfo.mbb.yale.edu/genome/ Alignment Sequence and structure based sequence alignment AlignMe 283 http://www.bioinfo.mpg.de  ... 
doi:10.1016/b978-0-12-409547-2.11133-3 fatcat:mf5ms2yylbburgrdihq5xpjhye

Alignment of multiple protein structures based on sequence and structure features

M.S. Madhusudhan, B. M. Webb, M. A. Marti-Renom, N. Eswar, A. Sali
2009 Protein Engineering Design & Selection  
Here, we align the sequences of multiple protein structures by a dynamic programming optimization of a scoring function that is a sum of an affine gap penalty and terms dependent on various sequence and  ...  Comparing the structures of proteins is crucial to gaining insight into protein evolution and function.  ...  Funding This work was supported by the National Institutes of Health (R01 GM54762-11, U54 GM62529).  ... 
doi:10.1093/protein/gzp040 pmid:19587024 pmcid:PMC2909824 fatcat:ztc3rqxlvnfurbviufhbbj57iy

Macromolecular Databases – A Background of Bioinformatics

Tibor Toth, Donatella Verbanac, Dubravko Jelić
2003 Food Technology and Biotechnology  
We would like to express our gratitude to the editors of databases for their courtesy and permission to introduce the database logos, pictures, tables and diagrams within this paper.  ...  Boris Mildner for their great help and critical assessment of this work.  ...  protein structures or domain organization of proteins [A.  ... 
doaj:bbe088d5f4874cb4a5ec2c7432482957 fatcat:dia4wh55inb2dgfp37zco5eg5i
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