In addition to what I have already said in this post, here are some additional points that highlight the astounding similarity.
A little backstory summarized: This is regarding Ron Zuckermann’s (RZ) recent paper that has been published online in January and will be included in the next issue of the journal 3DP+. After I reached out, Editor-in-Chief of journal, Skylar Tibbits, has argued that ‘similarities are to be expected’ because RZ was the last author of my publication on Peppytides. This is not acceptable. First I have started this work before I started working with RZ (read the history here). Plus, I have been extremely discriminated and bullied by RZ and my work (and career) was taken over, besides gaslighting me with ‘this work is not science’ (read the details starting in Part1 of my story-series). Now RZ is essentially duplicating that work and making a ‘simplified model’. Tibbits had further said that his journal is not the venue where I can highlight how similar this work is with mine, and any further complaint that I have, should be taken to Berkeley Lab for ‘arbitration’ and ‘investigation’, and that it is not under his journal’s ‘jurisdiction’. He said that he has made his decision after discussions with Berkeley Lab and the ethics team of his journal’s publisher, along with the authors.
Now a few points on similarities:
- The layout of this paper has been taken from my paper, including all section names and layouts.
- The naming of the model(Skeletide) sounds similar to (and rhymes with) my model name(Peppytide).
- This paper is essentially describing a simplified version of my model, with more coarse-graining, using straight lines instead of atoms. (including the scaling approximation – mine is 9.3mm/Å. vs theirs at the similar scale, only slightly modified, of approx. 7mm/Å)
- The authors mention that their model is a simpler version, but there is a glaring absence of the source of this approach to protein modeling to mirror Angstrom level biophysical forces in protein folding (my body of work).
- As I mentioned in Part 7: Authors mention several times about their work being a simpler version … but they never explain “simpler” to what? Or “simplifications” from what? “Simplified” form of what? That information is missing throughout the paper, a gross oversight of the foundational prior work they have built upon. Some examples:
- “The simplified model consists of amino acid units, which can be linked together …”
- “To focus on these model elements, we made inherent simplifications with regard to …”
- “We realized that there is a need for a new, simplified molecular protein model …”
- “… and to simplify construction.”
- “Here, we set out to develop a new, simplified protein model that …”
- Authors use the technique developed by me for designing, 3D printing, making, assembling and analyzing the model. Moreover, as in my models, the focus is on folding and on secondary structures.
- 8,000 PDB files have been used for analysis in this paper, a subset of what I had used (78,000 PDB files). The data extraction process and python scripting for the PBD file formats is based upon my work.
- Citation needed: In Section Turn Piece, “a hinge design was implemented, which allows the …” – This sort of hinge design is already published in my paper (PeppyChain) (see my paper on PeppyChain – Citation: Chakraborty P. PeppyChains: Simplifying the assembly of 3D-printed generic protein models. Arxiv 2015. arXiv:1605.04166).
- Authors have used something called pseudo-Ramachandran plot (c-alpha vs. dihedral) to highlight regions of alpha-helix and beta-sheet activity. This approach is similar to what I had used in my work: Ramachandran plot (the two dihedrals, phi vs. psi) to highlight regions of alpha-helix, beta-sheet, pi-helix and left-handed helix activity.
- Authors: “Similar to how peptide conformation can be fully described by analysis of the monomer dihedral angles in a Ramachandran plot, a protein …”
- A more accurate narration would be:
- “Chakraborty’s Peppytides were based on how peptide conformation can be fully described by analysis of the monomer dihedral angles in a Ramachandran plot, calculated from about 78,000 PDB files, from which the rotational barriers of the dihedral angles were calculated for alpha helix and beta sheet conformations and implemented with magnet arrays. Similar to that analysis, a protein …”
- Authors focus on alpha helix (red), beta sheet, both parallel and altiparallel (blue), turn (black) structures. This is a subset of structures that I had demonstrated in my work.
- Reference list looks inspired by my bibliographies. It might be a complete coincidence, but similar to my paper, the citation list starts with Dill and ends with Tibbits.
- Many sentences are similar. There is an overarching similarity of language that suggests a strong inspiration from my work and words. While I am not going to point out the exhaustive list of all such sentences , I am listing a few here as illustrative sampling:
- 1. Authors have used: “The Skeletide model developed here underlines the most fundamental aspects of protein secondary structure by depicting: (1) the skeletal alpha carbon trace and (2) an accurate representation of long-range intra-main chain H-bonding interactions.”
- I had used: “The Peppytide model developed here reproduces several critical aspects of the natural system that impact chain dynamics including the following: (i) dimensional accuracy of bond lengths and bond angles, (ii) a faithful representation of the short-range rotational barrier imposed on all of the backbone dihedral angles, and (iii) long-range stabilization resulting from intrabackbone hydrogen bonding.”
- 2. Authors: “We envision future versions of this model to include attachable side chains that interact with each other and to further tune the relative strengths of interconnects.”
- Me: “An obvious next step is to expand to the full set of amino acid side chains, so that a complete protein tertiary structure can be folded.”
- 3. Authors (a somewhat weaker version): “While this property nicely illustrates the modularity of protein structure—that a single structural unit can be linked together to form a larger, regular secondary structure—it does not accurately mimic the protein folding process in biology.”
- Me: “Although the current Peppytide model is a good tool for studying and teaching polypeptide chain folding, it also illustrates a fundamental architectural principle ubiquitous in biology: that a linear chain of modular units can be configured into a fantastic variety of 3D shapes.”
- 4. Authors: “Therefore, we focus here on dimensionally accurate modular subunits, we call Skeletides, that can (1) link together in predefined geometries using strong magnetic interconnects to create the alpha carbon skeletal backbone and (2) form long-range hydrogen bonds through weaker magnetic interactions. Side chains were omitted to draw attention to the underlying backbone architecture and to simplify construction.”
- Me: “With this vision in mind, we report here the design and fabrication of a tangible, coarse-grained, dimensionally accurate, physical molecular model of the polypeptide chain, which has the necessary degrees of freedom and bond rotational barriers to accurately emulate the backbone folding dynamics of the polypeptide chain.”
- 5. Authors: “We realized that there is a need for a new, simplified molecular protein model made from modular building blocks (amino acids) that would reveal the most universal, underlying aspects of protein architectures and be simple enough to readily assemble entire protein domains.”
- Me: “There is a strong need for scaled, realistically foldable, but inexpensive, physical models to go hand-in-hand with the AR and other computer interfaces, … Our approach was to break down the component amino acids into constituent coarse-grained components linked by rotatable bonds. The flexibility of the backbone chain in our model has made it possible to readily build all of the common protein secondary structure elements.”
These are MY words and MY vision that are re-worded and re-used in this paper, that I had developed over the years and hence it has the backstory as I detailed in the History post mentioned at the top.
- Conclusively, the authors have built on top of my work, but they cite my work in a very dismissive, degrading manner: “Peppytides are another example of a dynamic multicomponent physical model …” – This is unacceptable.
In conclusion, the authors have thoroughly and exhaustively used my methods, research directions and publications to develop their work and to write the paper. Any mention of that is missing (or intentionally absent). Further, Editor’s action in this matter is decisively absent.