Zobrazeno 1 - 10
of 23
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:
Chunlei Liu, Renata C. Geer, Kenneth J. Addess, Anna R. Panchenko, Lewis Y. Geer, Thomas Madej, Stephen H. Bryant, Aron Marchler-Bauer, Christopher J. Lanczycki, Shennan Lu, Jie Chen, Jessica H. Fong, Dachuan Zhang, Yanli Wang, Paul A. Thiessen
Publikováno v:
Nucleic Acids Research
Close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3D) structure by standard sequence similarity searches. Potentially, a great deal can be learned about proteins or protein families of in
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
Publikováno v:
Nucleic Acids Research
The sequencing of complete genomes has created a pressing need for automated annotation of gene function. Because domains are the basic units of protein function and evolution, a gene can be annotated from a domain database by aligning domains to the
Autor:
Anna R. Panchenko, Saikat Chakrabarti, Christopher J. Lanczycki, Teresa M. Przytycka, Stephen H. Bryant, Paul A. Thiessen
Publikováno v:
Nucleic Acids Research
Accurate multiple sequence alignments of proteins are very important to several areas of computational biology and provide an understanding of phylogenetic history of domain families, their identification and classification. This article presents a n
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:
Stephen F. Altschul, Stephen H. Bryant
Publikováno v:
Current Opinion in Structural Biology. 5:236-244
The past two years have seen the rapid development of new recognition methods for protein structure prediction. These algorithms ‘thread’ the sequence of one protein through the known structure of another, looking for an alignment that correspond