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Biology and Biochemistry

D-Index
73
Citations
25905
World Ranking
5827
National Ranking
146

Overview

Anastassis Perrakis is affiliated with Antoni van Leeuwenhoek Hospital in the Netherlands. Their research primarily focuses on biochemistry, genetics, and molecular biology, with significant contributions spanning subfields such as molecular biology, materials chemistry, cell biology, computational theory and mathematics, and genetics.

The scientist's work encompasses a variety of topics within molecular and cellular sciences. Notable areas include:

  • Protein Structure and Dynamics
  • Enzyme Structure and Function
  • Sphingolipid Metabolism and Signaling
  • Endoplasmic Reticulum Stress and Disease
  • RNA and protein synthesis mechanisms
  • Computational Drug Discovery Methods
  • Microtubule and mitosis dynamics

Many of the research outputs appear in journals and venues central to structural biology, molecular biochemistry, and related fields. Frequent publication venues include:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Acta Crystallographica Section D Structural Biology
  • Journal of Visualized Experiments
  • Protein Science
  • Nature

The following are selected recent papers authored or coauthored by Anastassis Perrakis, illustrating the range and focus of their scholarship:

  • "The CCP4 suite: integrative software for macromolecular crystallography," 2023, Acta Crystallographica Section D Structural Biology
  • "AlphaFill: enriching AlphaFold models with ligands and cofactors," 2022, Nature Methods
  • "AI revolutions in biology," 2021, EMBO Reports
  • "A Global Ramachandran Score Identifies Protein Structures with Unlikely Stereochemistry," 2020, Structure
  • "Tryptophan depletion results in tryptophan-to-phenylalanine substitutants," 2022, Nature

Collaborations appear to play a substantial role in their scientific activities. Frequent coauthors include:

  • Robbie P. Joosten
  • Maarten L. Hekkelman
  • Fernando Salgado-Polo
  • Ida de Vries
  • Razvan Borza

Best Publications

  • Automated protein model building combined with iterative structure refinement.

    Anastassis Perrakis;Richard Morris;Victor S. Lamzin

  • Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7.

    Gerrit G Langer;Serge X Cohen;Victor S Lamzin;Anastassis Perrakis

  • The PDB_REDO server for macromolecular structure model optimization.

    Robbie P. Joosten;Fei Long;Garib N. Murshudov;Anastassis Perrakis

  • RNA-binding protein Dnd1 inhibits microRNA access to target mRNA.

    Martijn Kedde;Markus J. Strasser;Bijan Boldajipour;Joachim A.F. Oude Vrielink

  • The crystal structure of DNA mismatch repair protein MutS binding to a G x T mismatch.

    Meindert H. Lamers;Anastassis Perrakis;Jacqueline H. Enzlin;Jacqueline H. Enzlin;Herrie H. K. Winterwerp

  • Developments in the CCP4 molecular-graphics project

    Liz Potterton;Stuart McNicholas;Eugene Krissinel;Jan Gruber

  • wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models.

    A. Perrakis;T. K. Sixma;K. S. Wilson;V. S. Lamzin

  • ARP/wARP and automatic interpretation of protein electron density maps.

    Richard J Morris;Anastassis Perrakis;Victor S Lamzin

  • ARP/wARP and molecular replacement

    Anastassis Perrakis;Maria Harkiolaki;Keith S. Wilson;Victor S. Lamzin

  • Crystal structure of a bacterial chitinase at 2.3 Å resolution

    Anastassis Perrakis;Ivo Tews;Zbigniew Dauter;Amos B Oppenheim

  • A New Generation of Crystallographic Validation Tools for the Protein Data Bank

    Randy J. Read;Paul D. Adams;W. Bryan Arendall;Axel T. Brunger

  • Structure and E3-ligase activity of the Ring–Ring complex of Polycomb proteins Bmi1 and Ring1b

    Gretel Buchwald;Petra van der Stoop;Oliver Weichenrieder;Anastassis Perrakis

  • Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay-Sachs disease.

    Ivo Tews;Anastassis Perrakis;Amos Oppenheim;Zbigniew Dauter

  • Structure of a cephalosporin synthase

    Karin Valegård;Anke C. Terwisscha van Scheltinga;Matthew D. Lloyd;Takane Hara

  • Substrate-Assisted Catalysis Unifies Two Families of Chitinolytic Enzymes

    Ivo Tews;Anke C. Terwisscha van Scheltinga;Anastassis Perrakis;Keith S. Wilson

  • Structural basis of substrate discrimination and integrin binding by autotaxin

    Jens Hausmann;Satwik Kamtekar;Evangelos Christodoulou;Jacqueline E Day

  • ARP/wARP's model-building algorithms. I. The main chain.

    Richard J. Morris;Anastassis Perrakis;Victor S. Lamzin

  • Ptprj is a candidate for the mouse colon-cancer susceptibility locus Scc1 and is frequently deleted in human cancers.

    Claudia A.L. Ruivenkamp;Tom van Wezel;Carlo Zanon;Alphons P.M. Stassen

  • Towards rationalization of crystallization screening for small- to medium-sized academic laboratories: the PACT/JCSG+ strategy

    J. Newman;D. Egan;T.S. Walter;R. Meged

  • Polo-like Kinase-1 Controls Proteasome-Dependent Degradation of Claspin during Checkpoint Recovery

    Ivan Mamely;Marcel A. T. M. van Vugt;Veronique A. J. Smits;Jennifer I. Semple

Frequent Co-Authors

Victor S. Lamzin
Victor S. Lamzin European Bioinformatics Institute
Titia K. Sixma
Titia K. Sixma Antoni van Leeuwenhoek Hospital
Wouter H. Moolenaar
Wouter H. Moolenaar Antoni van Leeuwenhoek Hospital
Keith S. Wilson
Keith S. Wilson University of York
Joel L. Sussman
Joel L. Sussman Weizmann Institute of Science
Geert J. P. L. Kops
Geert J. P. L. Kops Royal Netherlands Academy of Arts and Sciences
René H. Medema
René H. Medema Princess Máxima Center
Stavros J. Hamodrakas
Stavros J. Hamodrakas National and Kapodistrian University of Athens
Kees Jalink
Kees Jalink Antoni van Leeuwenhoek Hospital
Paul D. Adams
Paul D. Adams Lawrence Berkeley National Laboratory

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