- BIOINFORMATICS🔍
- BIOINFORMATICS ORIGINAL PAPER🔍
- REC protein family expansion by the emergence of a new signaling ...🔍
- Protein sequence motifs🔍
- Evolution of domain–peptide interactions to coadapt specificity and ...🔍
- Improving pairwise comparison of protein sequences with domain ...🔍
- Supervised Protein Family Classification and New Family Construction🔍
- Where Natural Protein Sequences Stand out From Randomness🔍
Exhaustive Enumeration of Protein Domain Families
DPCfam: a new method for unsupervised protein family classification
The Pfam protein families database in 2019, NAR, № 47, с. D427; Exhaustive enumeration of protein domain families, JMB, № 328, с. 749 https://doi.org ...
... protein families in 114 microbial genomes. BMC Bioinformatics, 5, 45. Heger,A. and Holm,L. (2003) Exhaustive enumeration of protein domain families. J. Mol ...
BIOINFORMATICS ORIGINAL PAPER - CiteSeerX
(2004) The Pfam protein families database. Nucleic Acids Res.,. 32, D138 ... (2003b) Exhaustive enumeration of protein domain families. J. Mol. Biol ...
REC protein family expansion by the emergence of a new signaling ...
(C and D) Amino acid sequences of the REC domains were aligned and separated into two distinct groups (AAA+ or GerE) based on the identity of ...
Protein sequence motifs, active or functional sites, and functional ...
Conduct exhaustive intermediate profile searches of a set of homologous protein sequences. ... Identify protein families and domains for a given protein sequence.
DOMpro: Protein Domain Prediction Using Profiles, Secondary ... - UCI
secondary structure elements and profiles. Bioinformatics, , In press. Heger,A. and Holm,L. (2003) Exhaustive enumeration of protein domain families.
Meta-DP: domain prediction meta-server - Internet Archive Scholar
Identification of domains in proteins can also be useful in structure determina- ... (2003) Exhaustive enumeration of protein domain families.J. Mol. Biol., 328 ...
Evolution of domain–peptide interactions to coadapt specificity and ...
... family of protein domains. To our knowledge, we have developed the first strategy to exhaustively enumerate all possible linear peptides and ...
Improving pairwise comparison of protein sequences with domain ...
To test this hypothesis, we compared the size of the new domain to that of the Pfam family that most resembles it. Surprisingly for the domains ...
Supervised Protein Family Classification and New Family Construction
6, 1889–1918. ... Heger A.Holm L.2003. Exhaustive enumeration of protein domain familiesJ. Mol. Biol.328749-767. Heger, A., and Holm, L. 2003.
Where Natural Protein Sequences Stand out From Randomness
Searches for such differences have hitherto focused on the exhaustive enumeration ... domains was obtained by assigning ECOD families to regions in the protein.
Progress towards mapping the universe of protein folds
Heger A, Holm L: Exhaustive enumeration of protein domain families. J Mol Biol. 2003, 328: 749-767. 10.1016/S0022-2836(03)00269-9. Article ...
Protein domain identification methods and online resources
tein can be classified into a corresponding family through search- ing the available protein domain family databases. ... Exhaustive enumeration of protein domain ...
What are protein domains? | Protein classification - EMBL-EBI
An example of a protein that contains multiple SH3 domains is the cytoplasmic protein Nck. Nck belongs to the adaptor family of proteins and it is involved in ...
DOMpro: Protein Domain Prediction Using Profiles, Secondary ...
and Holm, L., 2003. Exhaustive enumeration of protein domain families. Journal of Molecular Biology, 328:749-767. ... Holm, L. and Sander, C. 1994. Parser for ...
Fuzzy Sequence Pattern Searching for Proteins
algorithms, (2) Exhaustive enumeration algorithms, and (3) Heuristic methods. ... Sequence data of eleven protein families from Swiss-Prot Protein Database [15] ...
On the Origin of Protein Superfamilies and Superfolds - Nature
It is well known from observation of protein sequence and structure databases that distributions of protein sequences, families and folds are ...
Complete Combinatorial Mutational Enumeration of a protein ... - HAL
As a proof of concept, we applied CCME to the ACE2 binding site of the SARS-CoV-2 spike protein receptor binding domain. We selected ...
The Pfam protein families database Punta, Marco
(2003) Exhaustive enumeration of protein domain families. J. Mol. Biol., 328, 749–767. 2. The UniProt Consortium. (2010) The Universal ...
REC protein family expansion by the emergence of a new signaling ...
The evolution of protein domain families. Biochem Soc Trans 37:751–755 ... Exhaustive enumeration of protein domain families. J Mol Biol 328:749–767 ...