Popular BioServers

SWAKK is for detecting amino acid sites or regions of a protein under positive selection. It estimates the ratio of non-synonymous to synonymous substitution rates (K(A)/K(S)) between a pair of protein-coding DNA sequences, by sliding a 3D window, or sphere, across one reference structure. The program displays the results on the 3D protein structure.

JAFA is the Joined Assembly of Function Annotations, a protein function prediction meta-server. JAFA accepts a protein sequence as input, queries several function prediction programs, and produces results assembled from these servers.

GeneFisher is a software tool for selection of primers for the polymerase chain reaction (PCR). It goes beyond other available tools by designing degenerate primers for an unknown target from a family of homologue sequences.

Binding Affinity Prediction of Protein-Ligand (BAPPL) server computes the binding free energy of a non-metallo protein-ligand complex using an all atom energy based empirical scoring function.

Neural network and weight matrix prediction methods for protein sequences.

A tool in the understanding of limited proteolysis.The program works by calculating a series of prediction parameters for a given protein structure and then processing them to produce a final prediction score for each amino acid residue in a protein chain. This is achieved by averaging parameter scores for each residue position over a moving window. Hence, likely sites of limited proteolysis on a known protein structure from the Brookhaven databank can be assigned on this basis.

SIFT (Sorting Intolerant From Tolerant) is a program that predicts whether an amino acid substitution affects protein function so that users can prioritize substitutions for further study

Prediction of Subcellular Localization in Proteins (pSLIP) is a Support Vector Machines based algorithm that uses multiple physicochemical properties of amino acids to predict protein subcellular localization in eukaryotes across six different locations, namely, chloroplast, cytoplasmic, extracellular, mitochondrial, nuclear and plasma membrane.

SNPAnalyzer is a software that performs four essential statistical analyses of SNPs in a common computational environment.

A bench-mark for evaluation of protein multiple sequence alignment accuracy.