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(PS)2 Protein Structure Prediction Server performs automated homology modeling by combining PSI-BLAST, IMPALA, and T-Coffee for template selection and target-template alignment. The final three-dimensional (3D) structure is built using RAMP or MODELLER.
Align-m is an accurate and highly versatile multiple alignment program. It consists of 3 modules, S2P, P2P and P2M (see figure, manual), which can be used separately or consecutively to accomplish several tasks.
The AlphaPred server predicts the alpha turn residues in the given protein sequence. The method is based on the neural network training on PSI-BLAST generated position specific matrices and PSIPRED predicted secondary structure.
The Berkeley Phylogenomics Group provides a series of
web servers for phylogenomic analysis: classification of sequences to pre-computed families and subfamilies using the PhyloFacts Phylogenomic Encyclopedia, FlowerPower clustering of proteins sharing the same domain architecture, MUSCLE multiple sequence alignment, SATCHMO simultaneous alignment and tree construction, and SCI-PHY subfamily identification.
The aim of BetaTPred2 server is to predict ß turns in proteins from multiple alignment by using neural network from the given amino acid sequence. For ß turn prediction, it uses the position specific score matrices generated by PSI-BLAST and secondary structure predicted by PSIPRED.
The aim of BTEVAL server is to evaluate beta turn prediction algorithms on a uniform data set of 426 proteins or subsets of these proteins. It is the new data set in which no two protein chains have more that 25% sequence identity and each chain contains minimum one beta turn.
A multiple protein structure alignment server which creates an all-to-all pairwise alignment using a combinatorial extension program and then using Monte Carlo optimization methods conducts an iterative global optimization. Results are formatted using JOY.
The CHpredict server predict two types of interactions: C-H...O and C-H...π interactions. For C-H...O interaction, the server predicts the residues whose backbone Cα atoms are involved in interaction with backbone oxygen atoms and for C-H...π interactions, it predicts the residues whose backbone Cα atoms are involved in interaction with π ring system of side chain aromatic moieties.