✦ LIBER ✦

Knowledge-based interaction potentials for proteins

✍ Scribed by Atipat Rojnuckarin; Shankar Subramaniam

Publisher: John Wiley and Sons
Year: 1999
Tongue: English
Weight: 291 KB
Volume: 36
Category: Article
ISSN: 0887-3585
DOI: 10.1002/(sici)1097-0134(19990701)36:1<54::aid-prot5>3.0.co;2-b

No coin nor oath required. For personal study only.

✦ Synopsis

We discuss the derivation of atomic-level potentials of mean force from the known protein structures and their applicability for structural evaluation applications. In the derivation process, rigorous density estimation methodology is used to estimate the probability density functions (PDFs) for the distributions of interatomic distances in the protein structures. Potentials of mean force are then derived from these density functions using simple Boltzmann's relation. We also test the potentials against pairs of current and superseded protein structures in the Protein Data Bank. Using PDF potentials to evaluate each structure pair, we are able to identify, with high accuracy, which of the two structures is of higher resolution or better quality. This result shows that the PDF potentials are sensitive to details in protein structures as the current and superseded atomic coordinates generally do not differ by more than 1 Å in root-mean-square deviation, and that the PDF potentials could potentially be used for X-ray structure refinement and protein structure prediction. Proteins 1999

📜 SIMILAR VOLUMES

Interaction potentials for protein foldi

Interaction potentials for protein folding

✍ Flavio Seno; Amos Maritan; Jayanth R. Banavar 📂 Article 📅 1998 🏛 John Wiley and Sons 🌐 English ⚖ 56 KB 👁 2 views

We outline a general strategy for determining the effective coarse-grained interactions between the amino acids of a protein from the experimentally derived nativestate structures. The method is, in principle, free from any adjustable or empirically determined parameters, and it is tested on simple

NMR-Based Protein Potentials

✍ Dr. Da-Wei Li; Prof. Rafael Brüschweiler 📂 Article 📅 2010 🏛 John Wiley and Sons 🌐 English ⚖ 384 KB

NMR-Based Protein Potentials

✍ Dr. Da-Wei Li; Prof. Rafael Brüschweiler 📂 Article 📅 2010 🏛 John Wiley and Sons 🌐 English ⚖ 381 KB

A consistent empirical potential for wat

A consistent empirical potential for water–protein interactions

✍ Jan Hermans; Herman J. C. Berendsen; Wilfred F. Van Gunsteren; Johan P. M. Postm 📂 Article 📅 1984 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 275 KB 👁 1 views

## Abstract A simple point‐charge potential, developed earlier for the calculation of intermolecular forces in molecular‐dynamics simulations of liquid water, has been extended to include interactions between water molecules and polar groups of proteins. A complete potential for use in the simulati

Sustained performance of knowledge-based

Sustained performance of knowledge-based potentials in fold recognition

✍ Francisco S. Domingues; Walter A. Koppensteiner; Markus Jaritz; Andreas Prlic; C 📂 Article 📅 1999 🏛 John Wiley and Sons 🌐 English ⚖ 282 KB 👁 1 views

We describe the results obtained using fold recognition techniques in our third participation in the CASP experiment. The approach relies on knowledge-based potentials for alignment production and fold identification. As indicated by the increase in alignment quality and fold identification reliabil

Are knowledge-based potentials derived f

Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino acid types?

✍ Shamil R. Sunyaev; Frank Eisenhaber; Patrick Argos; Eugene N. Kuznetsov; Vladimi 📂 Article 📅 1998 🏛 John Wiley and Sons 🌐 English ⚖ 421 KB 👁 1 views

The parametric description of residue environments through solvent accessibility, backbone conformation, or pairwise residue-residue distances is the key to the comparison between amino acid types at protein sequence positions and residue locations in structural templates (condition of protein seque