New Paper in the Journal Cell Discovery

Congratulation to Dr. Chunli Yan who published a new paper combining computational modeling and cryo-electron microscopy to unveil structures of pre-initiation complexes of RNA Polymerase III. Han, Y.; Yan, C.; Fishbain, S.; Ivanov, I. & He, Y. Structural visualization of RNA polymerase III transcription machineries. Cell Discovery (2018) (in press)

New Paper in Proceedings of the National Academy of Sciences USA

Congratulation to Tom Dodd, Chunli Yan, Kurt Martin and Brad Kossmann who published a new paper in the journal Proceedings of the National Academy of Sciences USA.  Dodd, T.; Yan, C.; Kossmann, B.R.; Martin, K.; & Ivanov I. Uncovering universal rules governing the selectivity of the archetypal DNA glycosylase TDG Proceedings of the National Academy of Sciences USA (2018) doi:10.1073/pnas.1803323115 […]

A new paper in Nature Communications

Congratulations to Chunli Yan who published as a co-author on a new paper in the journal Nature Communications entitled “Rational design of a protein that binds integrin αvβ3 outside the ligand binding site”. The paper reports a new desinged protein which targets integrn at a novel site outside the canonocal Arg-Gly-Asp (RGD) binding site.

A new drug discovery paper published in Bioorganic & Medicinal Chemistry Letters

Congratulations to Brad Kossmann who published a new paper in the journal Bioorganic & Medicinal Chemistry Letters entitled “Discovery of selective inhibitors of tyrosyl-DNA phosphodiesterase 2 by targeting the enzyme DNA-binding cleft”. The paper details the characterization of three new selective inhibitors of the enzyme tyrosyl-DNA phosphodiesterase 2 (TDP2). TDP2processes protein/DNA adducts resulting from abortive DNA topoisomerase II […]

Ancient protein flexibility can drive ‘new’ functions

Scientists reveal how evolutionary fine-tuning has obscured the origin of the glucocorticoid receptor’s ability to adopt different shapes. It highlights how proteins that evolve ‘new’ functions may have had those capacities — in some cases, for millions of years — because of their flexibility. Source: Ancient protein flexibility can drive ‘new’ functions

Researchers unveil new, detailed images of DNA transcription

An unprecedented molecular view of the critical early events in gene expression, a process essential for all life, has been provided by researchers in a new study. Cryo-electron microscopy (cryo-EM), a technique that studies samples at cryogenic temperatures, combined with state-of-the-art computational modeling, allowed researchers to visualize large transcription pre-initiation complexes (PIC) at near-atomic resolution. […]

New paper in PLOS Computational Biology

Our paper ‘Alkylpurine Glycosylase D Employs DNA Sculpting as a Strategy to Extrude and Excise Damaged Bases’ was published in PLOS Computational Biology. We employed chain-of-replicas path optimization strategy to determine a minimum energy path (MEP) for flipping out a 3-methyl adenine lesion by the DNA glycosylase AlkD. The path showed that AlkD acts by […]

Another paper in Nucleic Acids Research

Our paper ‘Opening Pathways of the DNA Clamps Proliferating Cell Nuclear Antigen and Rad9-Rad1-Hus1’ has just been accepted by the journal Nucleic Acids Research. The recently solved structures of the DNA clamp protein 9-1-1 led to competing proposals regarding how 9-1-1 is loaded onto DNA. Through detailed subunit interface analysis, we identified the subunit interface […]

New paper in Nucleic Acids Research

Our paper ‘Probing DNA clamps with single-molecule force spectroscopy’ has just been published in Nucleic Acids Research and sheds light on the mechanisms of DNA clamp opening under external forces by combining molecular simulation with single-molecule micromanipulation experiments.

New PNAS paper on FEN1/DNA clamp complexes

Our collaborative efforts with Berkeley/LBNL have led to a combined experimental/computational publication ‘Repair complexes of FEN1, DNA and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability’ currently in press in Proceedings of the National Academy of Science U.S.A.

Our PNAS paper on PCNA ubiquitylation was highlighted

Our PNAS paper on PCNA ubiquitylation has been selected and evaluated by the post-publication peer review service Faculty of 1000 (F1000). According to the F1000 service this places our work in “.. the top 2% of published articles in biology and medicine”. The Oak Ridge Leadership Computing Facility at Oak Ridge National Laboratory highlights our […]


Our renewal proposal through the DOE INCITE initiative was awarded 4,000,000 CPU hours at the leadership computing facility at ORNL. We are gratified that the award exceeded our original request by 400,000 units For more details about the award refer to the new DOE Office of Science.

INCITE Proposal

A renewal proposal for computational resources through the DOE INCITE initiative has been submitted (07/01/2009). In 2009 our research project entitled “Interplay of AAA+ molecular machines, DNA repair enzymes and sliding clamps at the replication fork: A multiscale approach to modeling replisome assembly and function” was competitively chosen to receive 2,600,000 CPU hours of supercomputing […]