Hidden Markov models for detecting remote protein homologies.
MOTIVATION: A new hidden Markov model method (SAM-T98) for finding remote homologs
of protein sequences is described and evaluated. The method begins with a single target …
of protein sequences is described and evaluated. The method begins with a single target …
Protein multiple sequence alignment
Protein sequence alignment is the task of identifying evolutionarily or structurally related
positions in a collection of amino acid sequences. Although the protein alignment problem …
positions in a collection of amino acid sequences. Although the protein alignment problem …
CD150 association with either the SH2-containing inositol phosphatase or the SH2-containing protein tyrosine phosphatase is regulated by the adaptor protein …
LM Shlapatska, SV Mikhalap, AG Berdova… - The Journal of …, 2001 - journals.aai.org
Abstract CD150 (SLAM/IPO-3) is a cell surface receptor that, like the B cell receptor, CD40,
and CD95, can transmit positive or negative signals. CD150 can associate with the SH2 …
and CD95, can transmit positive or negative signals. CD150 can associate with the SH2 …
FoldRec-C2C: protein fold recognition by combining cluster-to-cluster model and protein similarity network
J Shao, K Yan, B Liu - Briefings in bioinformatics, 2021 - academic.oup.com
As a key for studying the protein structures, protein fold recognition is playing an important
role in predicting the protein structures associated with COVID-19 and other important …
role in predicting the protein structures associated with COVID-19 and other important …
ProtFold-DFG: protein fold recognition by combining Directed Fusion Graph and PageRank algorithm
J Shao, B Liu - Briefings in Bioinformatics, 2021 - academic.oup.com
As one of the most important tasks in protein structure prediction, protein fold recognition has
attracted more and more attention. In this regard, some computational predictors have been …
attracted more and more attention. In this regard, some computational predictors have been …
Strategies for multiple sequence alignment
HB Nicholas Jr, AJ Ropelewski, DW Deerfield - Biotechniques, 2002 - Taylor & Francis
We present an overview of multiple sequence alignments to outline the practical
consequences for the choices among different techniques and parameters. We begin with a …
consequences for the choices among different techniques and parameters. We begin with a …
Common fold in helix–hairpin–helix proteins
X Shao, NV Grishin - Nucleic acids research, 2000 - academic.oup.com
Abstract Helix–hairpin–helix (HhH) is a widespread motif involved in non-sequence-specific
DNA binding. The majority of HhH motifs function as DNA-binding modules, however, some …
DNA binding. The majority of HhH motifs function as DNA-binding modules, however, some …
Vibrio cholerae O139 genomes provide a clue to why it may have failed to usher in the eighth cholera pandemic
T Ramamurthy, AK Pragasam, A Taylor-Brown… - Nature …, 2022 - nature.com
Cholera is a life-threatening infectious disease that remains an important public health issue
in several low and middle-income countries. In 1992, a newly identified O139 Vibrio …
in several low and middle-income countries. In 1992, a newly identified O139 Vibrio …
Cellular assays identify barriers impeding iron-sulfur enzyme activity in a non-native prokaryotic host
Abstract Iron-sulfur (Fe-S) clusters are ancient and ubiquitous protein cofactors and play
irreplaceable roles in many metabolic and regulatory processes. Fe-S clusters are built and …
irreplaceable roles in many metabolic and regulatory processes. Fe-S clusters are built and …
Scoring hidden Markov models
Motivation Statistical sequence comparison techniques, such as hidden Markov models and
generalized profiles, calculate the probability that a sequence was generated by a given …
generalized profiles, calculate the probability that a sequence was generated by a given …