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NMR processing:
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NMR assignment:
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Side-chains:
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NOEs:
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UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
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BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
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Refinement:
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Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
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CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
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Secondary structure from chemical shifts:
CSI (via RCI server)
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MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
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RPF scores
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Chemical shifts:
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CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
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Protein geomtery:
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PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
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MetaMQAPII
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STAN
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Verify_3D
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NMR spectrum prediction:
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Methyl S2
B-factor
Molecular dynamics:
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Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


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  #1  
Unread 04-21-2011, 11:16 AM
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Default Not-NMR: interesting comments about article "Fix the PhD" in Nature

See the article here

Comments:

B. B. Goel:

Quote:
Many faculties attract students with utter lies, engage them as cheap, sometimes even free labor (which is supported by many universities, by making such free labor "mandatory" for the student, as per course requirements). Majority of faculties have NO intension to do any meaningful research to teach those students and postdocs to solve any real world problem, to develop novel drugs, or new technology or novel plant variety that can resist biotic or abiotic stress and so on. They are just used to generate, mostly, meaningless data- just for publications. Any invention or innovation is a mere coincidence or byproduct.
After a grueling PhD and postdoc tenure, they are not of much good for most of the jobs, except academic ones (to keep the same cycle rolling). That's why the rate of innovation and invention is becoming rarer in any field of biology. Big companies are cutting down its R&D units simply because THERE ARE NOT MANY USEFUL CANDIDATES TO INNOVATE OR INVENT REAL DRUGS OR TECHNOLOGIES OR PLANT VARIETIES AFTER "SUCCESSFULLY" COMPLETING THE ASSEMBLY LINE OF SO-CALLED ACADEMIC RESEARCH. The actual talented people are meticulously weeded out by this ruthless majority of mediocrity, promoted by the universities, government regulatory agencies and also by funding agencies.

Xianfa Xie:

Quote:
the mass production of PhDs, particularly in life sciences over the last few decades, has not only increased competition but created a bad competing environment and academic culture: It favors quick and dirty publications with erroneous or unfounded claims over publications with comprehensive analysis, solid arguments, and correct conclusions, creating an academic environment selecting the mediocre, which can produce something seemingly scientific, but against the outstanding scientists that are really creative, knowledgeable, and solid in research.

Such an academic environment has generated and is continuing to generate tons of trash publications polluting science and requiring even more efforts to clean them up. However, lies repeated a thousand times might be accepted as truth, sometimes unfounded scientific ideas could go on to dominate a field for a long time, seriously inhibiting real scientific progress.

Trash research has also damaged the reputation of science and scientists as a whole, incurring a lot of ridiculing of scientists and backslash of the public on scientific research in recent years
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  #2  
Unread 04-22-2011, 08:26 PM
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Yet another interesting comment:

By Rex Williams:

Quote:
Nothing will change until the supply/demand inequality and incentive structures are changed. Admission to programs needs to be severely constrained. Grad students and Postdocs need to be excused when they fail to meet strict milestones, which cuts the cost to the research budgets and helps smart and talented young people develop meaningful careers at the same time. Tenure needs to be eliminated so that existing faculty are made to have to compete with up-and-coming scientists, preventing them from getting complacent. Additionally, I would advocate for actual penalties to be placed on PIs that consistently fail to turn out good people that contribute meaningfully to science and technology; whether that is in academia, government, or industry is not important. Perhaps when a PI is made to realize that the consequences for being a poor advisor and using people up are an inability to continue to win funding, they will be much more selective and cautious of the people that they invite into their lab and how they develop them.

While other professionals have the potential to create jobs, scientists and engineers have the potential to create entire industries, an economic impact that absolutely justifies the spending of government money on research. A PhD is supposed to be the pinnacle of scholarly achievement and should be near unattainable by anyone but the very brightest and most talented, thereby the most likely to deliver a substantial public benefit. The current system provides little chance to fulfill either and American taxpayers are paying dearly for this. I doubt it will be able to continue much longer.
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