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Predicting protein function from sequence and structural data
JD Watson, RA Laskowski, JM Thornton - Current opinion in structural …, 2005 - Elsevier
When a protein's function cannot be experimentally determined, it can often be inferred from
sequence similarity. Should this process fail, analysis of the protein structure can provide …
sequence similarity. Should this process fail, analysis of the protein structure can provide …
Structure-based function prediction: approaches and applications
The ever increasing number of protein structures determined by structural genomic projects
has spurred much interest in the development of methods for structure-based function …
has spurred much interest in the development of methods for structure-based function …
A method for localizing ligand binding pockets in protein structures
The accurate identification of ligand binding sites in protein structures can be valuable in
determining protein function. Once the binding site is known, it becomes easier to perform in …
determining protein function. Once the binding site is known, it becomes easier to perform in …
Automated prediction of ligand‐binding sites in proteins
We present a method, termed AutoLigand, for the prediction of ligand‐binding sites in
proteins of known structure. The method searches the space surrounding the protein and …
proteins of known structure. The method searches the space surrounding the protein and …
AutoSite: an automated approach for pseudo-ligands prediction—from ligand-binding sites identification to predicting key ligand atoms
Motivation: The identification of ligand-binding sites from a protein structure facilitates
computational drug design and optimization, and protein function assignment. We introduce …
computational drug design and optimization, and protein function assignment. We introduce …
Design of compound libraries based on natural product scaffolds and protein structure similarity clustering (PSSC)
Recent advances in structural biology, bioinformatics and combinatorial chemistry have
significantly impacted the discovery of small molecules that modulate protein functions …
significantly impacted the discovery of small molecules that modulate protein functions …
Automated discovery of 3D motifs for protein function annotation
Motivation: Function inference from structure is facilitated by the use of patterns of residues
(3D motifs), normally identified by expert knowledge, that correlate with function. As an …
(3D motifs), normally identified by expert knowledge, that correlate with function. As an …
Protein structure similarity clustering (PSSC) and natural product structure as inspiration sources for drug development and chemical genomics
Finding small molecules that modulate protein function is of primary importance in drug
development and in the emerging field of chemical genomics. To facilitate the identification …
development and in the emerging field of chemical genomics. To facilitate the identification …
Looking at enzymes from the inside out: The proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme–ligand …
A Ben-Shimon, M Eisenstein - Journal of Molecular Biology, 2005 - Elsevier
Analysis of the distances of the exposed residues in 175 enzymes from the centroids of the
molecules indicates that catalytic residues are very often found among the 5% of residues …
molecules indicates that catalytic residues are very often found among the 5% of residues …
Large-scale prediction of protein structure and function from sequence
The identification of novel drug targets from genomic data involves the large-scale analysis
of many protein sequences. Methods for automated structure and function prediction are an …
of many protein sequences. Methods for automated structure and function prediction are an …