Functional classification using phylogenomic inferenceThe COMBREX project: design, methodology, and initial results.Phylogenomic inference of protein molecular function: advances and challengesModBase, a database of annotated comparative protein structure models, and associated resourcesThe interface of protein structure, protein biophysics, and molecular evolutionThe PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classificationGetting started in structural phylogenomicsStandardized benchmarking in the quest for orthologsFlowerPower: clustering proteins into domain architecture classes for phylogenomic inference of protein function.Automated protein subfamily identification and classification.ResBoost: characterizing and predicting catalytic residues in enzymesArabidopsis thaliana PGR7 encodes a conserved chloroplast protein that is necessary for efficient photosynthetic electron transport.Active site prediction using evolutionary and structural information.Predicted hexameric structure of the Agrobacterium VirB4 C terminus suggests VirB4 acts as a docking site during type IV secretion.Molecular characterization of proteolytic cleavage sites of the Pseudomonas syringae effector AvrRpt2.SATCHMO-JS: a webserver for simultaneous protein multiple sequence alignment and phylogenetic tree construction.Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA)Ortholog identification in the presence of domain architecture rearrangement.PhyloFacts: an online structural phylogenomic encyclopedia for protein functional and structural classification.Distribution and properties of the genes encoding the biosynthesis of the bacterial cofactor, pyrroloquinoline quinone.Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis.The Generation Challenge Programme comparative plant stress-responsive gene catalogue.Berkeley PHOG: PhyloFacts orthology group prediction web serverINTREPID: a web server for prediction of functionally important residues by evolutionary analysisINTREPID--INformation-theoretic TREe traversal for Protein functional site IDentification.From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants.Subfamily hmms in functional genomics.Simultaneous sequence alignment and tree construction using hidden Markov models.Proteome analysis of the rice etioplast: metabolic and regulatory networks and novel protein functions.Arabidopsis downy mildew resistance gene RPP27 encodes a receptor-like protein similar to CLAVATA2 and tomato Cf-9.
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P50
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American bio-engineer
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