Pavel Afonine

Computational Research Scientist

Molecular Biophysics and Integrated Bioimaging

Structural Biology

Building: 33, Room 349
Mail Stop: 33R0345
Phone: (510) 221-7384
Fax: (510) 486-5909
PAfonine@lbl.gov

Programs & Initiatives

Computational Crystallography Initiative (CCI)
PHENIX Software Suite
Quantum Refinement Project

Research Interests

1) New algorithms and methods development for crystallographic structure determination of small- and macro(bio)-molecules.

2) Software (Phenix) development for automated crystallographic structure solution, analysis and validation using X-ray, neutron and cryo-EM data.

3) Three-dimensional structure determination of macro-molecules.

Selected Publications

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Congratulations to Biosciences Area Director’s Award Recipients

September 22, 2021

Numerous Biosciences Area personnel are among the 2021 Berkeley Lab Director’s Awards honorees. This annual program recognizes outstanding contributions by employees to all facets of Lab activities. A complete list of winners can be found here. The 10th annual Director’s Awards ceremony will take place on November 18 at noon.

Revealing the Shapes of Molecular Machines

January 29, 2019

Within each cell of the human body, thousands of molecular machines are at work. They transport nutrients and biochemicals into and out of our cells, build other tiny machines, and even move our cells around. To understand how these molecular machines work, scientists create three-dimensional pictures using electron cryomicroscopy (cryo-EM), catching these machines in different shapes that give insight into their function. Now researchers at Berkeley Lab and their international collaborators who write and distribute the Phenix software suite have developed a new set of computational tools for automated structure determination from cryo-EM data.

A Near-Atomic Resolution Map of a Key DNA Protein Complex

September 14, 2017

Molecular Biophysics and Integrated Bioimaging (MBIB) Division scientists led by Eva Nogales have resolved the 3-D structure of a critical human cellular protein complex involved in DNA transcription and repair at an unprecedented level of resolution. The complex, called transcription factor IIH (TFIIH), unzips the DNA double helix so that genes can be accessed and read. Malfunctions of the complex are associated with premature aging, cancer propensity, and a variety of other defects. One challenge with solving the structure of TFIIH has been that it exists in such minute amounts that it is difficult to produce and purify in large quantities. Moreover, once obtained, it may not form crystals suitable for X-ray diffraction. The researchers used cryo-electron microscopy (cryo-EM), a technique in which purified samples are flash-frozen at ultra cold temperatures, and which works even on very small quantities. “The fact that we resolved this protein structure from human cells makes this even more relevant to disease research,” said Nogales. Basil Greber, a postdoctoral fellow in Nogales’s lab, was first author on the study published in the journal Nature. Computational research scientist Pavel Afonine and MBIB Division Director Paul Adams also contributed to the project. Read more from the Berkeley Lab News Center.

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