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. 


  • 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.


  • 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.
  • 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.


  • 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. 
Be Sociable, Share!

Enjoyed this Post ?

Subscribe by E-mail:

Subscribe in a reader. Follow us on twitter.

  • Iddo Friedberg

    “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:

    The perspectives comment:

  • Nir London

    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.

  • John

    I poke through them.

  • Lev Gorenstein

    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.

  • Rich Apodaca

    Not so much reading, but scanning. Not exactly my field, but interesting.

    Question: any possibility of including a DOI link for each item?

  • Enrico

    “I wonder if anybody really reads these digests ?!?!” Absolutely; been following since your first post, always inspiring.

  • Eric Donaldson

    I read it this time

  • Chris

    Loving the digest! Needs links though, even if they are behind a pay wall for most folks…

  • admin

    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 ?

  • Masha Niv

    Hi Nir,
    I am reading these and I think it’s great you are doing this!

  • Fabian

    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.


  • Fabian

    … used to work in … :-)

  • Hannes

    i read that stuff

  • Iddo Friedberg

    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.

  • Raj

    Good work Nir, keep it up and what’s up with the ego boost (need responses)?

  • Anders

    I read it. The comments too. I agree that google analytics is great! :o)

  • Pepe Subirana


    Most useful!! Thank you for these Digests Nir.


  • Mickey Kosloff

    Late is better than never?!
    Keep ’em coming Nir :-)

Powered by WordPress | Aeros Theme | WordPress Themes
© 2009 Rosetta Design Group LLC