FINDSITE-metal: Integrating evolutionary information and machine learning for structure-based metal-binding site prediction at the proteome level

Metalloproteomes: A Bioinformatic Approach

(2009) Claudia Andreini et al.   ACCOUNTS OF CHEMICAL RESEARCH

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

(2009) Shashi Pandit et al.   BMC BIOINFORMATICS

FINDSITE: a combined evolution/structure-based approach to protein function prediction

(2009) J. Skolnick et al.   BRIEFINGS IN BIOINFORMATICS

Protein structure prediction and model quality assessment

(2009) Andriy Kryshtafovych et al.   DRUG DISCOVERY TODAY

Evolutionary Trace Annotation of Protein Function in the Structural Proteome

(2009) Serkan Erdin et al.   JOURNAL OF MOLECULAR BIOLOGY

Metalloproteins

(2009) Joshua Finkelstein   NATURE

Function and biogenesis of iron–sulphur proteins

(2009) Roland Lill   NATURE

Comparison of structure-based and threading-based approaches to protein functional annotation

(2009) Michal Brylinski et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Template-free protein structure prediction and quality assessment with an all-atom free-energy model

(2009) Srinivasa Murthy Gopal et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

(2009) John A. Capra et al.   PLoS Computational Biology

Protein function annotation by homology-based inference

(2009) Yaniv Loewenstein et al.   GENOME BIOLOGY

Sequence-based feature prediction and annotation of proteins

(2009) Agnieszka S Juncker et al.   GENOME BIOLOGY

Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination

(2008) Ivan Dokmanić et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Prediction of zinc-binding sites in proteins from sequence

(2008) Nanjiang Shu et al.   BIOINFORMATICS

I-TASSER server for protein 3D structure prediction

(2008) Yang Zhang   BMC BIOINFORMATICS

High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies

(2008) Jean-Marc Aury et al.   BMC GENOMICS

Fast procedure for reconstruction of full-atom protein models from reduced representations

(2008) Piotr Rotkiewicz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Protein-folding location can regulate manganese-binding versus copper- or zinc-binding

(2008) Steve Tottey et al.   NATURE

DBD-Hunter: a knowledge-based method for the prediction of DNA–protein interactions

(2008) Mu Gao et al.   NUCLEIC ACIDS RESEARCH

Prediction of 3D metal binding sites from translated gene sequences based on remote-homology templates

(2008) Ronen Levy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs

(2008) Arlo Randall et al.   BMC STRUCTURAL BIOLOGY

Preservation of protein clefts in comparative models

(2008) David Piedra et al.   BMC STRUCTURAL BIOLOGY

Occurrence of Copper Proteins through the Three Domains of Life: A Bioinformatic Approach

(2007) Claudia Andreini et al.   JOURNAL OF PROTEOME RESEARCH