Deep learning for computational chemistry
The rise and fall of artificial neural networks is well documented in the scientific literature of
both computer science and computational chemistry. Yet almost two decades later, we are …
both computer science and computational chemistry. Yet almost two decades later, we are …
Comparing proteins by their internal dynamics: Exploring structure–function relationships beyond static structural alignments
C Micheletti - Physics of life reviews, 2013 - Elsevier
The growing interest for comparing protein internal dynamics owes much to the realisation
that protein function can be accompanied or assisted by structural fluctuations and …
that protein function can be accompanied or assisted by structural fluctuations and …
The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures
A Andreeva, E Kulesha, J Gough… - Nucleic acids …, 2020 - academic.oup.com
Abstract The Structural Classification of Proteins (SCOP) database is a classification of
protein domains organised according to their evolutionary and structural relationships. We …
protein domains organised according to their evolutionary and structural relationships. We …
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 …
PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations
Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the
coding regions are frequently associated with the development of various genetic diseases …
coding regions are frequently associated with the development of various genetic diseases …
Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols …
By using different evaluation strategies, we systemically evaluated the performance of
Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular …
Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular …
SCOPe: Structural Classification of Proteins—extended, integrating SCOP and ASTRAL data and classification of new structures
NK Fox, SE Brenner, JM Chandonia - Nucleic acids research, 2014 - academic.oup.com
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 …
Domain enhanced lookup time accelerated BLAST
GM Boratyn, AA Schäffer, R Agarwala, SF Altschul… - Biology direct, 2012 - Springer
Background BLAST is a commonly-used software package for comparing a query sequence
to a database of known sequences; in this study, we focus on protein sequences. Position …
to a database of known sequences; in this study, we focus on protein sequences. Position …
CATH: comprehensive structural and functional annotations for genome sequences
The latest version of the CATH-Gene3D protein structure classification database (4.0,
http://www. cathdb. info) provides annotations for over 235 000 protein domain structures …
http://www. cathdb. info) provides annotations for over 235 000 protein domain structures …
ECOD: an evolutionary classification of protein domains
Understanding the evolution of a protein, including both close and distant relationships,
often reveals insight into its structure and function. Fast and easy access to such up-to-date …
often reveals insight into its structure and function. Fast and easy access to such up-to-date …