NMR chemical shifts in proteins depend strongly on local structure. The program TALOS establishes an empirical relation between 13C, 15N and 1H chemical shifts and backbone torsion angles ϕ and ψ (Cornilescu et al. J Biomol NMR 13 289–302, 1999). Extension of the original 20-protein database to 200 proteins increased the fraction of residues for which backbone angles could be predicted from 65 to 74%, while reducing the error rate from 3 to 2.5%. Addition of a two-layer neural network filter to the database fragment selection process forms the basis for a new program, TALOS+, which further enhances the prediction rate to 88.5%, without increasing the error rate. Excluding the 2.5% of residues for which TALOS+ makes predictions that strongly differ from those observed in the crystalline state, the accuracy of predicted ϕ and ψ angles, equals ±13°. Large discrepancies between predictions and crystal structures are primarily limited to loop regions, and for the few cases where multiple X-ray structures are available such residues are often found in different states in the different structures. The TALOS+ output includes predictions for individual residues with missing chemical shifts, and the neural network component of the program also predicts secondary structure with good accuracy.

/pdf/talos-a-hybrid-method-for-predicting-protein-backbone-4t5z8ivciv.pdf

TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts.

We describe a simple and inexpensive method to produce super-hydrophobic surfaces on aluminum and its alloy by oxidation and chemical modification. Water or aqueous solutions (pH = 1−14) have contact angles of 168 ± 2 and 161 ± 2° on the treated surfaces of Al and Al alloy, respectively. The super-hydrophobic surfaces are produced by the cooperation of binary structures at micro- and nanometer scales, thus reducing the energies of the surfaces. Such super-hydrophobic properties will greatly extend the applications of aluminum and its alloy as lubricating materials.

Stable biomimetic super-hydrophobic engineering materials.

Spinach--a software library for simulation of spin dynamics in large spin systems.

https://users.cs.duke.edu/~brd/Teaching/Bio/asmb/Papers/NMR/Introduction-reviews/Guntert03a.pdf

Automated NMR protein structure calculation

A selective classified bibliography of symbolic computation in some areas of chemistry is provided together with some examples of computer algebra algorithms and techniques to facilitate future joint work of chemists and computer scientists. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004

Symbolic calculation in chemistry: Selected examples

One-dimensional $S=1$ $\mathrm{XXZ}$ chains with uniaxial single-ion-type anisotropy are studied by numerical exact diagonalization of finite-size systems. The numerical data are analyzed using conformal field theory, the level spectroscopy, phenomenological renormalization-group, and finite-size scaling method. We thus present a quantitatively reliable ground-state phase diagram of this model. The ground states of this model contain the Haldane phase, large-D phase, N\'eel phase, two $\mathrm{XY}$ phases, and the ferromagnetic phase. There are four different types of transitions between these phases: the Brezinskii-Kosterlitz-Thouless-type transitions, the Gaussian-type transitions, the Ising-type transitions, and the first-order transitions. The locations of these critical lines are accurately determined.

https://arxiv.org/pdf/cond-mat/0209403.pdf

Ground-state phase diagram of S = 1 XXZ chains with uniaxial single-ion-type anisotropy

Multipole NMR. X. Multispin, multiquantum, multilinear operator bases

Multipole NMR. VII. Bromine NMR quadrupolar echoes in crystalline KBr

A sequential assignment protocol for proteins was developed using heteronuclear 3D NMR. The protocol consists of an amino acid type recognition algorithm and a primary sequence mapping algorithm. The former measures the similarity between each detected spin pattern and 20 standard amino acid coupling patterns. Both chemical shift and topologically likeness are considered. The mapping algorithm uses the amino acid type information to direct detected polypeptides to proper position onto protein primary sequence. The assignment protocol can be applied to spin systems generated by many different approaches. We designed a few computer programs to derive a protein's backbone and side chain spin systems using heteronuclear 3D NMR. The results was then input to the sequential assignment protocol. All of the algorithms were tested on NMR data of a 90-residue N-domain of chicken skeletal troponin-C.

Bryan C. Sanctuary

Papers

Ground-state phase diagram of S = 1 XXZ chains with uniaxial single-ion-type anisotropy

Multipole NMR. X. Multispin, multiquantum, multilinear operator bases

Multipole NMR. VII. Bromine NMR quadrupolar echoes in crystalline KBr

Automated Resonance Assignment of Proteins Using Heteronuclear 3D NMR. 2. Side Chain and Sequence-Specific Assignment

Multipole NMR. IX. Polar graphical representation of nuclear spin polarizations