Bi-weekly Digest 27/03/09
In this Bi-weekly digest a novel O2 transport protein designed from first principals (on which we’ll elaborate in an upcoming post – stay tuned) and a nice over-representation of Bioinformatics papres.
Nature:
- Design and engineering of an O(2) transport protein. Koder RL, Anderson JL, Solomon LA, Reddy KS, Moser CC, Dutton PL.
- Transmembrane passage of hydrophobic compounds through a protein channel wall. Hearn EM, Patel DR, Lepore BW, Indic M, van den Berg B.
Journal of Computational Biology:
- Optimizing Energy Potential for Protein Fold Recognition with Parametric Evaluation Function. Junfeng Gu et al.
Proteins:
- A new prediction strategy for long local protein structures using an original description. Aurélie Bornot, Catherine Etchebest, Alexandre G. de Brevern.
- REMO: A new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Yunqi Li, Yang Zhang.
- A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins. Peter Májek, Ron Elber
- Graphical models of protein-protein interaction specificity from correlated mutations and interaction data. John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg
Biophysical Journal:
- Protein structure prediction by pro-Sp3-TASSER. Zhou H, Skolnick J.
- Coupling between normal modes drives protein conformational dynamics: illustrations using allosteric transitions in myosin II. Zheng W, Thirumalai D.
JMB:
- Structural alphabets for protein structure classification: a comparison study. Le Q, Pollastri G, Koehl P.
- Predicting Protein Function and Binding Profile via Matching of Local Evolutionary and Geometric Surface Patterns. Tseng YY, Dundas J, Liang J.
- Structural and Functional Studies of the Biotin Protein Ligase from Aquifex aeolicus Reveal a Critical Role for a Conserved Residue in Target Specificity. Cecile M. Tron, Iain W. McNae, Margaret Nutley, David J. Clarke, Alan Cooper, Malcolm D. Walkinshaw, Robert L. Baxter, Dominic J. Campopiano
- Sequence and Structural Features of Enzymes and their Active Sites by EC Class. Bray T, Doig AJ, Warwicker J.
- Signatures of protein-DNA recognition in free DNA binding sites. Locasale JW, Napoli AA, Chen S, Berman HM, Lawson CL.
Bioinformatics:
- Double water exclusion : a hypothesis refining the O-ring theory for the hot spots at protein interfaces. Jinyan Li and Qian Liu.
- Sequence-based prediction of protein interaction sites with an integrative method. Xue-wen Chen and Jong Cheol Jeong
- Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics. Lee-Wei Yang, Eran Eyal, Ivet Bahar, and Akio Kitao.
- The protein–small-molecule database, a non-redundant structural resource for the analysis of protein-ligand binding. Izhar Wallach and Ryan Lilien.
- Fragment-based identification of druggable hot spots of proteins using Fourier domain correlation techniques. Ryan Brenke, Dima Kozakov, Gwo-Yu Chuang, Dmitri Beglov, David Hall, Melissa R. Landon, Carla Mattos, and Sandor Vajda.
- DTA: dihedral transition analysis for characterization of the effects of large main-chain dihedral changes in proteins. Wataru Nishima, Guoying Qi, Steven Hayward, and Akio Kitao.
- SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements. Charles E. Chapple, Roderic Guigó, and Alain Krol.
- CPSP-web-tools: a server for 3D lattice protein studies. Martin Mann, Cameron Smith, Mohamad Rabbath, Marlien Edwards, Sebastian Will, and Rolf Backofen.
- MatrixDB, a database focused on extracellular protein–protein and protein–carbohydrate interactions. Emilie Chautard, Lionel Ballut, Nicolas Thierry-Mieg, and Sylvie Ricard-Blum.
I wonder if anybody really reads these digests ?!?! If you’re reading these lines, please post a comment to let us know. Even just you’re name, a ‘hi’, anything to let us know… cheers ; )
PLoS Computational Biology:
- Rapid Sampling of Molecular Motions with Prior Information Constraints. Barak Raveh et al.
- Conformational Changes and Slow Dynamics through Microsecond Polarized Atomistic Molecular Simulation of an Integral Kv1.2 Ion Channel. Pär Bjelkmar et al.
- Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins. Michael D. Daily et al.
- Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments. Vincent A. Voelz et al.
Nature Structural and Molecular Biology:
- The mechanism of folding of Im7 reveals competition between functional and kinetic evolutionary constraints. Claire T Friel, D Alastair Smith, Michele Vendruscolo, Joerg Gsponer and Sheena E Radford
Is there any specific paper you’d like to know more about? start a discussion? Tell us in the comments.
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“I wonder if anybody really reads these digests ?!?! If you’re reading these lines, please post a comment to let us know. Even just you’re name, a ‘hi’, anything to let us know… cheers ; )”
I don’t read your digests Nir. Had I actually been reading your digest, I would have noticed that the following paper, which I think is germane, is missing:
http://www.sciencemag.org/cgi/content/full/323/5921/1610
The perspectives comment:
http://www.sciencemag.org/cgi/content/full/323/5921/1567
It’s a good thing than that you’re not reading the digests, other wise it could have been embarrassing
Thanks for the heads up – I’ll update in a bit.
I poke through them.
No way, I’m not reading your digests, and writing this comment was just a spontaneous act of entropy!
Thanks for your work, Nir. The digests and other posts are very interesting and informative.
Not so much reading, but scanning. Not exactly my field, but interesting.
Question: any possibility of including a DOI link for each item?
“I wonder if anybody really reads these digests ?!?!” Absolutely; been following since your first post, always inspiring.
Thanks!
E.
I read it this time
Loving the digest! Needs links though, even if they are behind a pay wall for most folks…
Thanks everyone for the show of support. (or entropy
). I’ll revert to adding links or DOI starting from the next digest. I guess the next step would be thinking of a way to develop active discussion about one or two of the more interesting papers – sort of a world wide journal club. How do you suggest we go about this ?
Hi Nir,
I am reading these and I think it’s great you are doing this!
Hi Nir,
I am reading the digests and for me as someone who left the academic field they are of great value. The digests provide a nice overview on whats going on in the field I sued to work in and for at least 50%-60% of the presented publications I’ll read the abstract at the publishers website.
Thanks
Fabian
… used to work in …
i read that stuff
By the way, Google Analytics can give you a much better picture of how many people are reading your stuff and from where they hail.
Good work Nir, keep it up and what’s up with the ego boost (need responses)?
I read it. The comments too. I agree that google analytics is great!
)
BS”D
Most useful!! Thank you for these Digests Nir.
Pepe
Late is better than never?!
Keep ‘em coming Nir