doi.bio/pavel_v_afonine

Pavel V. Afonine

Overview

Pavel V. Afonine is a researcher specialising in computational biology and biochemistry. He has contributed to research in computer science, resolution (electron density), medicine, biology, and protein structure. Afonine has affiliations with the Lawrence Berkeley National Laboratory, University of California, Berkeley, and Shanghai University.

Notable Works

Afonine has co-authored 111 publications, with over 37,000 citations. Some of his notable works include:

• PHENIX: A comprehensive Python-based system for macromolecular structure solution, which minimises the need for manual interpretation of complex data and automates procedures.
• Phenix.refine: A program within the PHENIX package that supports crystallographic structure refinement with a wide range of parameters and customisations.
• Macromolecular structure determination using X-rays, neutrons and electrons: A paper describing recent developments in the Phenix software package for macromolecular structure determination.
• Real-space refinement in PHENIX for cryo-EM and crystallography: A paper that describes the implementation of real-space refinement in the phenixrealspacerefine program, which improves the refinement of atomic models.

Awards and Honours

Afonine has received the Biosciences Area Director's Award from Berkeley Lab in 2021.

Pavel V. Afonine

Overview

Pavel V. Afonine is a researcher specialising in computational biology and biochemistry. He has contributed to research in computer science, resolution (electron density), medicine, biology, and protein structure. Afonine has previously been affiliated with the Lawrence Berkeley National Laboratory, the University of California, Berkeley, and Shanghai University. He currently works at the Molecular Biophysics and Integrated Bioimaging (MBIB) Division of the Lawrence Berkeley National Laboratory.

Education

Afonine has a verified email address at lbl.gov, indicating that he likely has at least an undergraduate degree.

Research

Afonine's research focuses on computational methods for determining the structure of biological macromolecules, such as proteins and nucleic acids. He has developed algorithms and software for automated structure determination and refinement using techniques such as X-ray crystallography, neutron diffraction, and electron cryomicroscopy (cryo-EM). His work aims to minimise the need for manual interpretation of complex data and repetitive tasks, improving the efficiency and accuracy of structure determination.

Publications

Afonine has co-authored over 100 publications, with over 30,000 citations. Some of his notable publications include:

• "PHENIX: a comprehensive Python-based system for macromolecular structure solution" (2010) - This paper describes the PHENIX software for macromolecular structure determination, which provides a comprehensive system with an emphasis on automation.
• "Towards automated crystallographic structure refinement with phenix.refine" (2012) - This paper presents an overview of the phenix.refine program within the PHENIX package, which supports crystallographic structure refinement with a wide range of customisation options.
• "Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix" (2019) - This publication describes recent developments in the Phenix software package for macromolecular structure determination using X-rays, neutrons, and electrons.
• "Real-space refinement in PHENIX for cryo-EM and crystallography" (2018) - The paper describes the implementation of real-space refinement in the phenixrealspacerefine program, which allows for faster calculation and improved model refinement.

Awards and Honours

Afonine has received the Biosciences Area Director's Award from Berkeley Lab in 2021.