Zobrazeno 1 - 10
of 14
pro vyhledávání: '"Stephen H. Bryant"'
Autor:
Thomas, Madej, Aron, Marchler-Bauer, Christopher, Lanczycki, Dachuan, Zhang, Stephen H, Bryant
Publikováno v:
Methods in molecular biology (Clifton, N.J.). 2112
The VAST+ algorithm is an efficient, simple, and elegant solution to the problem of comparing the atomic structures of biological assemblies. Given two protein assemblies, it takes as input all the pairwise structural alignments of the component prot
Autor:
Stephen H. Bryant, Anna R. Panchenko
Publikováno v:
Protein Science. 11:361-370
Sequence comparison methods based on position-specific score matrices (PSSMs) have proven a useful tool for recognition of the divergent members of a protein family and for annotation of functional sites. Here we investigate one of the factors that a
Autor:
Farideh Chitsaz, Mikhail Mullokandov, Stephen H. Bryant, Siqian He, Jessica H. Fong, John B. Anderson, Fu-er Lu, Asba Tasneem, Myra K. Derbyshire, David I. Hurwitz, Renata C. Geer, Roxanne A. Yamashita, Carol DeWeese-Scott, James S. Song, Christopher J. Lanczycki, Zhaoxi Ke, Cynthia A. Liebert, Shennan Lu, Chunlei Liu, Dachuan Zhang, Noreen R. Gonzales, Naigong Zhang, Narmada Thanki, Lewis Y. Geer, John D. Jackson, Gabriele H. Marchler, Aron Marchler-Bauer, Marc Gwadz
Publikováno v:
Nucleic Acids Research
NCBI's Conserved Domain Database (CDD) is a collection of multiple sequence alignments and derived database search models, which represent protein domains conserved in molecular evolution. The collection can be accessed at http://www.ncbi.nlm.nih.gov
Autor:
Cynthia A. Liebert, David I. Hurwitz, Stephen H. Bryant, Gabriele H. Marchler, Paul A. Thiessen, Vahan Simonyan, James S. Song, Dachuan Zhang, Jodie J. Yin, John B. Anderson, Benjamin A. Shoemaker, John D. Jackson, Lewis Y. Geer, Carol DeWeese-Scott, Mikhail Mullokandov, Siqian He, Roxanne A. Yamashita, Christopher J. Lanczycki, Zhaoxi Ke, Chunlei Liu, Fu Lu, Aron Marchler-Bauer, Marc Gwadz, Praveen F. Cherukuri
Publikováno v:
Nucleic Acids Research
The Conserved Domain Database (CDD) is the protein classification component of NCBI's Entrez query and retrieval system. CDD is linked to other Entrez databases such as Proteins, Taxonomy and PubMed®, and can be accessed at http://www.ncbi.nlm.nih.g
Autor:
Aron Marchler-Bauer, Stephen H. Bryant
Publikováno v:
Nucleic Acids Research. 32:W327-W331
We describe the Conserved Domain Search service (CD-Search), a web-based tool for the detection of structural and functional domains in protein sequences. CD-Search uses BLAST(R) heuristics to provide a fast, interactive service, and searches a compr
Publikováno v:
Protein Science. 13:884-892
We present a method for prediction of functional sites in a set of aligned protein sequences. The method selects sites which are both well conserved and clustered together in space, as inferred from the 3D structures of proteins included in the align
Autor:
Dachuan Zhang, Manoj Tyagi, Anna R. Panchenko, Thomas Madej, Stephen H. Bryant, Ratna R. Thangudu
Publikováno v:
PLoS ONE, Vol 7, Iss 1, p e28896 (2012)
PLoS ONE
PLoS ONE
The coverage and reliability of protein-protein interactions determined by high-throughput experiments still needs to be improved, especially for higher organisms, therefore the question persists, how interactions can be verified and predicted by com
Autor:
Alejandro A. Schäffer, Stephen H. Bryant, Anna R. Panchenko, Paul A. Thiessen, Stephen F. Altschul, Maricel G. Kann
Publikováno v:
Bioinformatics (Oxford, England). 21(8)
Motivation: With the continuing rapid growth of protein sequence data, protein sequence comparison methods have become the most widely used tools of bioinformatics. Among these methods are those that use position-specific scoring matrices (PSSMs) to
Publikováno v:
Proteins. 48(3)
Profile search methods based on protein domain alignments have proven to be useful tools in comparative sequence analysis. Domain alignments used by currently available search methods have been computed by sequence comparison. With the growth of the
Autor:
Stephen H. Bryant, Benjamin A. Shoemaker, David I. Hurwitz, Cynthia A. Liebert, Gabriele H. Marchler, Jie Chen, Lewis Y. Geer, Paul A. Thiessen, Yanli Wang, Aron Marchler-Bauer, Thomas Madej, James S. Song, Siqian He, Anna R. Panchenko, John B. Anderson, Roxanne A. Yamashita
Publikováno v:
Nucleic acids research. 30(1)
Three-dimensional structures are now known within many protein families and it is quite likely, in searching a sequence database, that one will encounter a homolog with known structure. The goal of Entrez’s 3D-structure database is to make this inf