Non-alphanumeric characters (from '-') are stripped.
All search keyword are used in searching links: e.g. bioinformatics links directory will search for links that contain all three keywords in title, description, or tags.
You can search for an exact phrase by enclosing the query in quotes: e.g. "bioinformatics links directory"
e.g. Search query "genomic sequences" dna will search for links containing the phrase "genomic sequences" and dna.
You can include OR uppercase keyword: e.g. dna OR rna looks for keywords dna or rna.
You can include - prefix or NOT uppercase keyword to define keywords that should not be included: e.g. dna OR rna NOT protein (alternatively: dna OR rna -protein) will look for links with keywords DNA or RNA, but not protein
Online Guassian Network Model (oGNM) calculates the equilibrium dynamics of any structure submitted in PDB format, using the Gaussian Network Model (GNM), a network model for representing biomolecules.
Protein Blocks Expert (PBE) uses a structural alphabet of short structural motifs to compare protein structures. PBE uses as its structural alphabet a set of protein blocks derived from structurally aligned homologous proteins present in the PALI Database.
PEP-FOLD uses a hidden Markov model-derived structural alphabet for de novo modeling of 3D conformations of peptides between 9-25 amino acids in aqueous solution. Updates to PEP-FOLD allow for modeling of linear and disulphide bonded cyclic peptides with 9-36 amino acids using benchmarked peptides.
pepMMsMIMIC is a peptidomimetic compound virtual screening tool based on a multi-confromers 3D-similarity search strategy. Using as input the 3D structure of a peptide bound to a protein, pepMMsMIMIC suggests which chemical structures are able to mimic the protein-protein recognitiuon of this natural peptide using pharmacophore and shape similarity techniques.
Phosfinder uses a structural comparison algorithm to identify phosphate binding sites in protein structures. It scans a query structure in PDB format against a set of known 3D phosphate binding motifs and outputs a visual display of the predicted binding sites on the query protein structure.
PI2PE (Protein Interface/Interior Prediction Engine) consists of three predictors (WESA, cons-PPISP, and DISPLAR) for predicting solvent accessibility and interface residues from the structure of a protein-binding or DNA-binding protein.