Protein database searches using compositionally adjusted substitution matrices
SF Altschul, JC Wootton, EM Gertz… - The FEBS …, 2005 - Wiley Online Library
Almost all protein database search methods use amino acid substitution matrices for
scoring, optimizing, and assessing the statistical significance of sequence alignments. Much …
scoring, optimizing, and assessing the statistical significance of sequence alignments. Much …
Searching for hypothetical proteins: theory and practice based upon original data and literature
G Lubec, L Afjehi-Sadat, JW Yang, JPP John - Progress in neurobiology, 2005 - Elsevier
A large part of mammalian proteomes is represented by hypothetical proteins (HP), ie
proteins predicted from nucleic acid sequences only and protein sequences with unknown …
proteins predicted from nucleic acid sequences only and protein sequences with unknown …
SCOPe: improvements to the structural classification of proteins–extended database to facilitate variant interpretation and machine learning
Abstract The Structural Classification of Proteins—extended (SCOPe, https://scop. berkeley.
edu) knowledgebase aims to provide an accurate, detailed, and comprehensive description …
edu) knowledgebase aims to provide an accurate, detailed, and comprehensive description …
SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures
Abstract Structural Classification of Proteins—extended (SCOPe, http://scop. berkeley. edu)
is a database of protein structural relationships that extends the SCOP database. SCOP is a …
is a database of protein structural relationships that extends the SCOP database. SCOP is a …
Hidden Markov model speed heuristic and iterative HMM search procedure
LS Johnson, SR Eddy, E Portugaly - BMC bioinformatics, 2010 - Springer
Abstract Background Profile hidden Markov models (profile-HMMs) are sensitive tools for
remote protein homology detection, but the main scoring algorithms, Viterbi or Forward …
remote protein homology detection, but the main scoring algorithms, Viterbi or Forward …
GlobPlot: Exploring protein sequences for globularity and disorder
A major challenge in the proteomics and structural genomics era is to predict protein
structure and function, including identification of those proteins that are partially or wholly …
structure and function, including identification of those proteins that are partially or wholly …
SCOPe: classification of large macromolecular structures in the structural classification of proteins—extended database
Abstract The SCOPe (Structural Classification of Proteins—extended, https://scop. berkeley.
edu) database hierarchically classifies domains from the majority of proteins of known …
edu) database hierarchically classifies domains from the majority of proteins of known …
A comparative study of the relationship between protein structure and β-aggregation in globular and intrinsically disordered proteins
A growing number of proteins are being identified that are biologically active though
intrinsically disordered, in sharp contrast with the classic notion that proteins require a well …
intrinsically disordered, in sharp contrast with the classic notion that proteins require a well …
The ASTRAL compendium in 2004
The ASTRAL Compendium provides several databases and tools to aid in the analysis of
protein structures, particularly through the use of their sequences. Partially derived from the …
protein structures, particularly through the use of their sequences. Partially derived from the …
The relationship between sequence and interaction divergence in proteins
There is currently a gap in knowledge between complexes of known three-dimensional
structure and those known from other experimental methods such as affinity purifications or …
structure and those known from other experimental methods such as affinity purifications or …