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D-Index & Metrics

Chemistry

D-Index
84
Citations
30140
World Ranking
2777
National Ranking
66

Overview

Amedeo Caflisch is affiliated with the University of Zurich in Switzerland and has a substantial record of research contributions primarily in the field of Biochemistry, Genetics, and Molecular Biology. Their work spans several subfields, notably Molecular Biology, Materials Chemistry, Computational Theory and Mathematics, Physiology, and Cognitive Neuroscience.

The researcher focuses on topics such as RNA modifications and cancer, protein structure and dynamics, cancer-related gene regulation, computational drug discovery methods, protein degradation and inhibitors, RNA and protein synthesis mechanisms, and RNA research and splicing.

Among their recent papers are:

  • "Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation," 2021, Molecular Cell
  • "Proteostasis of Islet Amyloid Polypeptide: A Molecular Perspective of Risk Factors and Protective Strategies for Type II Diabetes," 2021, Chemical Reviews
  • "METTL3 Inhibitors for Epitranscriptomic Modulation of Cellular Processes," 2021, ChemMedChem
  • "Dynamic 3D proteomes reveal protein functional alterations at high resolution in situ," 2020, Cell
  • "Small-Molecule Inhibitors of METTL3, the Major Human Epitranscriptomic Writer," 2020, ChemMedChem

Caflisch frequently publishes in venues including bioRxiv (Cold Spring Harbor Laboratory), Journal of Chemical Information and Modeling, ACS Bio & Med Chem Au, The Journal of Physical Chemistry B, and ACS Medicinal Chemistry Letters. These journals reflect the multidisciplinary nature of their work, bridging computational chemistry, molecular biology, and medicinal chemistry.

They often collaborate with researchers such as R.K. Bedi, Yaozong Li, Danzhi Huang, Ioana M. Ilie, and Andreas Vitalis, indicating a broad network within their scientific community that supports interdisciplinary projects.

Best Publications

  • CHARMM: the biomolecular simulation program.

    B. R. Brooks;C. L. Brooks;A. D. Mackerell;L. Nilsson

  • Protein structure-based drug design: from docking to molecular dynamics.

    Paweł Śledź;Amedeo Caflisch

  • Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylketonuria.

    Lihi Adler-Abramovich;Lilach Vaks;Ohad Carny;Dorit Trudler

  • The protein folding network.

    Francesco Rao;Amedeo Caflisch

  • Evaluation of a fast implicit solvent model for molecular dynamics simulations

    Philippe Ferrara;Joannis Apostolakis;Amedeo Caflisch

  • Macrodomain-containing proteins are new mono-ADP-ribosylhydrolases.

    Florian Rosenthal;Karla L H Feijs;Emilie Frugier;Mario Bonalli

  • PARP1 ADP-ribosylates lysine residues of the core histone tails

    Simon Messner;Matthias Altmeyer;Hongtao Zhao;Andrea Pozivil

  • The role of side-chain interactions in the early steps of aggregation: Molecular dynamics simulations of an amyloid-forming peptide from the yeast prion Sup35

    Jörg Gsponer;Urs Haberthür;Amedeo Caflisch

  • FACTS: Fast analytical continuum treatment of solvation

    Urs Haberthür;Amedeo Caflisch

  • Wordom: a program for efficient analysis of molecular dynamics simulations

    Michele Seeber;Marco Cecchini;Francesco Rao;Giovanni Settanni

  • Interpreting the aggregation kinetics of amyloid peptides

    Riccardo Pellarin;Amedeo Caflisch

  • Multiple Copy Simultaneous Search and Construction of Ligands in Binding Sites: Application to Inhibitors of HIV- 1 Aspartic Proteinase

    Amedeo Caflisch;Andrew Miranker;Martin Karplus

  • Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces.

    Michele Seeber;Angelo Felline;Francesco Raimondi;Stefanie Muff

  • Predicting free energy changes using structural ensembles.

    Alexander Benedix;Caroline M Becker;Bert L de Groot;Amedeo Caflisch

  • Molecular dynamics in drug design.

    Hongtao Zhao;Amedeo Caflisch

  • Replica exchange molecular dynamics simulations of amyloid peptide aggregation.

    M. Cecchini;F. Rao;M. Seeber;A. Caflisch

  • Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water

    Joannis Apostolakis;Philippe Ferrara;Amedeo Caflisch

  • Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences.

    Gian Gaetano Tartaglia;Andrea Cavalli;Riccardo Pellarin;Amedeo Caflisch

  • ACID AND THERMAL DENATURATION OF BARNASE INVESTIGATED BY MOLECULAR DYNAMICS SIMULATIONS

    Amedeo Caflisch;Martin Karplus

  • Exhaustive docking of molecular fragments with electrostatic solvation.

    Nicolas Majeux;Marco Scarsi;Joannis Apostolakis;Claus Ehrhardt

  • Folding simulations of a three-stranded antiparallel β-sheet peptide

    Philippe Ferrara;Amedeo Caflisch

Frequent Co-Authors

Cristina Nevado
Cristina Nevado University of Zurich
Martin Karplus
Martin Karplus Harvard University
Andreas Plückthun
Andreas Plückthun University of Zurich
Peter Hamm
Peter Hamm University of Zurich
Ehud Gazit
Ehud Gazit Tel Aviv University
Gian Gaetano Tartaglia
Gian Gaetano Tartaglia Italian Institute of Technology
Philipp Schuetz
Philipp Schuetz University of Basel
Gottfried Otting
Gottfried Otting Australian National University
Siew Pheng Lim
Siew Pheng Lim A*STAR - Agency for Science, Technology and Research
Xun-Cheng Su
Xun-Cheng Su Nankai University

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