• Publications
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A family of macrodomain proteins reverses cellular mono-ADP-ribosylation
ADP-ribosylation is a reversible post-translational modification with wide-ranging biological functions in all kingdoms of life. A variety of enzymes use NAD+ to transfer either single or multipleExpand
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EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results
TLDR
The server application for discontinuous epitope prediction, EPSVR, uses a Support Vector Regression (SVR) method to integrate six scoring terms. Expand
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Multiple molecular architectures of the eye lens chaperone αB-crystallin elucidated by a triple hybrid approach
The molecular chaperone αB-crystallin, the major player in maintaining the transparency of the eye lens, prevents stress-damaged and aging lens proteins from aggregation. In nonlenticular cells, itExpand
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Prediction of antigenic epitopes on protein surfaces by consensus scoring
TLDR
We present a new antigen Epitope Prediction method, which uses ConsEnsus Scoring (EPCES) from six different scoring functions - residue epitope propensity, conservation score, side-chain energy score, contact number, surface planarity score, and secondary structure composition. Expand
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Protein–protein docking with a reduced protein model accounting for side‐chain flexibility
  • M. Zacharias
  • Chemistry, Medicine
  • Protein science : a publication of the Protein…
  • 1 June 2003
A protein–protein docking approach has been developed based on a reduced protein representation with up to three pseudo atoms per amino acid residue. Docking is performed by energy minimization inExpand
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Tapasin and other chaperones: models of the MHC class I loading complex
Abstract MHC (major histocompatibility complex) class I molecules bind intracellular virus-derived peptides in the endoplasmic reticulum (ER) and present them at the cell surface to cytotoxic TExpand
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Conformational flexibility of the MHC class I alpha1-alpha2 domain in peptide bound and free states: a molecular dynamics simulation study.
Major histocompatibility complex class I proteins play a key role in the recognition and presentation of peptide antigens to the host immune system. The structure of various major histocompatibilityExpand
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Effective Dephosphorylation of Src Substrates by SHP-1*
The protein-tyrosine phosphatase SHP-1 is a negative regulator of multiple signal transduction pathways. We observed that SHP-1 effectively antagonized Src-dependent phosphorylations in HEK293 cells.Expand
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A statistical analysis of random mutagenesis methods used for directed protein evolution.
We have developed a statistical method named MAP (mutagenesis assistant program) to equip protein engineers with a tool to develop promising directed evolution strategies by comparing 19 mutagenesisExpand
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Binding site prediction and improved scoring during flexible protein–protein docking with ATTRACT
The ATTRACT protein–protein docking program combined with a coarse‐grained protein model has been used to predict protein–protein complex structures in CAPRI rounds 13–19. For six targets acceptableExpand
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