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Macromolecular Modeling Blog (5 unread)

• March 04, 2010
• 13:27

  Literature Review 04/03/10

   » ‎ Macromolecular Modeling Blog
  Another compilation of forty some titles from the recent literature all about your favorite computational structural biology science. Two of the papers are by Rosetta Design Group's members - see if you can find waldo. Enjoy.

  
  

  
• February 28, 2010
• 4:52

  CAPRI: Selected Talks IV

   » ‎ Macromolecular Modeling Blog
  This is the fifth and last post in the CAPRI series, summarizing the presentations of Xiaoqin Zou and Ora Schueler-Furman (Saving the best for last..), as provided by the speakers. I hope the CAPRI series was able to give a snapshot of the state of computational protein-protein docking and its community. I want to thank again to everyone that took part in the meeting and helped me with this series.

  
  

  
• February 16, 2010
• 14:39

  Tradeoff between stability and multispecificity in the design of promiscuous proteins

   » ‎ Macromolecular Modeling Blog
  Traditionally, computational protein design efforts have been directed at calculating a single sequence predicted to fold to a particular target structure. Recently, however, a number of conceptual generalizations have been pursued, ranging from the use of backbone flexibility, off-rotamer side chain flexibility, negative design, multi-body potentials, conformational free energy, and prediction of sequence profiles. Below I present our state-of-the-art research whose goal is to understand how protein sequences are optimized to be compatible with binding multiple partners with high affinity. - By Menachem Fromer.

  
  

  
• February 15, 2010
• 11:17

  RosettaCon 2010

   » ‎ Macromolecular Modeling Blog
  As in previous years, we would like to invite representatives of the pharma and biotech industry to participate in RosettaCon 2010. Take part in the workshops, seminars, and have an opportunity to meet the Rosetta Commons researchers. Get to know Rosetta from the inside. RosettaCon will take place during August 3-6 at the beautiful Sleeping Lady Mountain Retreat in Leavenworth, Washington, about 2.5 hours outside Seattle, in a dramatic mountain scenery - the only fitting environment for a scientific discussion really.

  
  

  
• February 10, 2010
• 13:08

  Models on the cover

   » ‎ Macromolecular Modeling Blog
  In 2009, an israeli model (Bar Refaeli) had gotten the cover of the sports illustrated special swimsuit issue. In 2010, an israeli modeler had gotten the cover of the february issue of "Structure". Indeed it's hard to say which is more sexy.

  
  

  
• February 03, 2010
• 17:18

  Scientist in Computational Protein Design Position at Adimab

   » ‎ Macromolecular Modeling Blog
  Please submit a resume and cover letter to hr@adimab.com. Description Adimab is looking for scientists with experience in computational protein design to join its Computational Biology group. Successful candidates will work on developing novel computational algorithms and software for rational structure-based design and optimization of antibody molecules and libraries. The computational effort will be closely linked to [...]

  
  

  
• January 30, 2010
• 11:47

  CAPRI: Selected Talks III

   » ‎ Macromolecular Modeling Blog
  This is the fourth post in the CAPRI series, summarizing the presentations of Paul Bates, Martin Zacharias, and Carlos Camacho, as provided by the speakers. More to appear in the continuation of the series.

  
  

  
• January 22, 2010
• 3:36

  Literature Review 22/01/10

   » ‎ Macromolecular Modeling Blog
  You know the drill... a collection of relevant titles from the recent literature, if you want to discuss any of these, or expand on them, we'll be more than happy.

  
  

  
• January 17, 2010
• 12:08

  CAPRI: Selected Talks II

   » ‎ Macromolecular Modeling Blog
  This is the third post in the CAPRI series, summarizing the presentations of Jeffrey Gray, Zhiping Weng, and Miriam Eisenstein, as provided by the speakers. More to appear in the continuation of the series.

  
  

  
• January 14, 2010
• 9:31

  Barcelona BioMed Conference - Intrinsically Disordered Proteins in Biomedicine

   » ‎ Macromolecular Modeling Blog
  A meeting for everyone that liked this post (17 Protein disorder prediction servers): Dates: 4-6 October, 2010 Venue: Institut d’Estudis Catalans, Barcelona, Spain. Registration deadline: July 15, 2010.

  
  

  
• January 13, 2010
• 11:25

  What will become of PyMOL?

   » ‎ Macromolecular Modeling Blog
  Schrödinger announced several days ago that it has reached an agreement with the estate of the late Dr. Warren L. DeLano to continue the development, support, and sales of the PyMOL software package. PyMOL is well known to all of us in the field and is perhaps the most widely used and loved molecular visualization tool. [...]

  
  

  
• January 12, 2010
• 12:29

  CAPRI: Selected Talks I

   » ‎ Macromolecular Modeling Blog
  This is the second post in the CAPRI series, summarizing the presentations of Sandor Vajda, Alexandre Bonvin, and Julie Mitchell, as provided by the speakers. More to appear in the continuation of the series.

  
  

  
• January 11, 2010
• 13:52

  CAPRI or: What is the State of Protein-Protein Docking?

   » ‎ Macromolecular Modeling Blog
  This is the first post in a series, summarizing the CAPRI (Critical Assessment of PRediction of Interactions) 4th Evaluation meeting. In this post I'll try to give a more personal perspective of the experiment results, the state and trends of computational protein-protein docking and the vibes behind the scenes. The next posts in the series will shortly summarize select talks from the meeting, kindly provided by the speakers.

  
  

  
• January 04, 2010
• 6:51

  NAR 2010 DB issue - What’s in it for us?

   » ‎ Macromolecular Modeling Blog
  NAR just published the new special "Database" issue for 2010. We collected 23 papers that might be of interest to structural biologists, modelers and other protein people.

  
  

  
• January 02, 2010
• 4:54

  How to detect a forged PDB

   » ‎ Macromolecular Modeling Blog
  Most of you probably heard about the recent retraction of some 12 structures (1BEF, 1CMW, 1DF9/2QID, 1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0) from the PDB. Reported first by The University of Alabama at Birmingham and follwing by structural biology blogs as p212121 and ByteSizeBio - also known as "Structuregate". One question that arises is - was this preventable?

  
  

  
• December 30, 2009
• 11:20

  17 Protein disorder prediction servers

   » ‎ Macromolecular Modeling Blog
  Over the past decade it has become evident that many proteins have disordered regions, even in their native states. Moreover, entire proteins were found to be intrinsically disordered. We present here 17 webservers intended to predict disordered regions from protein sequence. Is your protein folded ?

  
  

  
• December 27, 2009
• 12:31

  Happy New Year

   » ‎ Macromolecular Modeling Blog
  Another year went by, and there is still modeling work to be done. 2009 was a good year for the “Macromolecular Modeling Blog”. The number of subscribers almost quadrupled. We have several hundreds of twitter followers, and a twitter modelers list. And best of all we are still enjoying what we do. What will happen in [...]

  
  

  
• December 08, 2009
• 14:37

  Macromolecular modeling n00bz, get up to speed with this review

   » ‎ Macromolecular Modeling Blog
  Last month in Nature Chemical Biology, Dan Mandell and Tanja Kortemme from UCSF published a great review of current research in macromolecular modeling and experimentation: Computer-aided design of functional protein interactions. The review focuses on protein-protein interactions and interfaces but also covers the general field of macromolecular modeling in some depth. It includes sections that [...]

  
  

  
• December 07, 2009
• 9:40

  NIH wants you to use “the World’s Most Powerful Supercomputer”

   » ‎ Macromolecular Modeling Blog
  The NIH recently announced a proposal solicitation for use of the Blue Waters petascale computing system. They will be giving a videocast on December 17th and of course molecular modeling is at the top of the list of priorities: “Because of the considerable NIGMS investment in protein folding and prediction of protein structure from sequence, we will [...]

  
  

  
• December 06, 2009
• 10:09

  Alternate structures and catalysis in cyclophilin

   » ‎ Macromolecular Modeling Blog
  A beautiful post by Michael Clarkson on a beautiful work by himself and friends, published in Nature. It's always nice when a fellow blogger get's to present his own work. Post is re-blogged as is from "Discount Thoughts".

  
  

  
• December 01, 2009
• 12:13

  Literature Digest

   » ‎ Macromolecular Modeling Blog
  50 papers of potential interest from the (very) recent literature.

  
  

  
• November 11, 2009
• 13:34

  PDB Widgets

   » ‎ Macromolecular Modeling Blog
  As from next week, the RCSB PDB will provide web widgets - small bits of code, which provide PDB functionality that you can embed in your own website. All of the widgets that are provided are 100% self contained JavaScript files and will be maintained by the RSCB PDB. We've taken some of those widgets for a test drive.

  
  

  
• November 10, 2009
• 10:47

  Molecular Modeling Jobs

   » ‎ Macromolecular Modeling Blog
  Several positions for molecular modelers have recently came to our attention. We thought some of our readers might express interest in these opportunities. If you find this type of service helpfull/annoying please let us know in the comments. If you wish to post available positions in the molecular modeling field please contact us.

  
  

  
• November 09, 2009
• 11:56

  PyRosetta

   » ‎ Macromolecular Modeling Blog
  The Gray Lab at Johns Hopkins University has just released PyRosetta, a Python-based interactive platform for accessing the objects and algorithms within the Rosetta protein structure prediction suite. In addition to the code, the Gray Lab has put together a book that leads the reader through basics of protein structure and energetics to applications in folding, [...]

  
  

  
• November 07, 2009
• 10:58

  Modeling literature digest - it’s back..

   » ‎ Macromolecular Modeling Blog
  After a long break, the molecular modeling literature digest is back with ~50 recent publication which we believe would be of interest. As usual you are most welcome to add relevant publications or suggest specific papers for us to focus on.