HotPoint: hot spot prediction server for protein interfaces

Download

index.pdf

Date

2010-07-01

Author

Tunçbağ, Nurcan
GÜRSOY, Attila

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

90
views

49
downloads

The energy distribution along the protein-protein interface is not homogenous; certain residues contribute more to the binding free energy, called 'hot spots'. Here, we present a web server, HotPoint, which predicts hot spots in protein interfaces using an empirical model. The empirical model incorporates a few simple rules consisting of occlusion from solvent and total knowledge-based pair potentials of residues. The prediction model is computationally efficient and achieves high accuracy of 70%. The input to the HotPoint server is a protein complex and two chain identifiers that form an interface. The server provides the hot spot prediction results, a table of residue properties and an interactive 3D visualization of the complex with hot spots highlighted. Results are also downloadable as text files. This web server can be used for analysis of any protein-protein interface which can be utilized by researchers working on binding sites characterization and rational design of small molecules for protein interactions. HotPoint is accessible at http://prism.ccbb.ku.edu.tr/hotpoint.

Subject Keywords

Binding-energy, Receptor, Database

URI

https://hdl.handle.net/11511/31892

Journal

NUCLEIC ACIDS RESEARCH

DOI

https://doi.org/10.1093/nar/gkq323

Collections

Graduate School of Informatics, Article

Suggestions

OpenMETU
Core

Polynomial solutions of the Schrodinger equation for the generalized Woods-Saxon potential Berkdemir, C; Berkdemir, A; Sever, Ramazan (American Physical Society (APS), 2005-08-01) The bound state energy eigenvalues and the corresponding eigenfunctions of the generalized Woods-Saxon potential are obtained by means of Nikiforov-Uvarov (NU) method. Certain bound states of the Schrodinger equation for the potential are calculated analytically and the wave functions are found in terms of the Jacobi polynomials. It is shown that the results are in good agreement with those obtained previously.
Simulating nutrient uptake dynamics in plankton models: A case study for the cilician basin marine ecosystem Akoğlu, Ekin (2020-01-01) The primary productivity in the Cilician Basin is severely constrained by phosphorus limitation due to high N:P ratios in the external nutrient inputs. Therefore, special attention is required when the dynamics of plankton is modelled. Acknowledging that mathematical formulation of nutrient uptake by phytoplankton in ecosystem models is crucial as it determines the degree of realism of the representation of biogeochemical dynamics, a plankton model was developed by utilising two widely adopted approaches; i...
Türkiye’nin osmotik enerji potansiyeli Özyurt Tarakcıoğlu, Gülizar; Korkmaz, Ahmet Berkan (null; 2018-11-30) Osmotik enerji, tuzluluk değişim farkına bağlı olarak yarı geçirgen zar arasındaki su moleküllerinin fiziksel hareketi sonucu elde edilen yenilenebilir bir enerji kaynağıdır. Osmotik enerji üretimi ise farklı iki konsantrasyona sahip su kaynaklarının özel yarı geçirgen membranlar ile ayrılarak, yoğun çözeltide artan su miktarının sahip olduğu potansiyel enerjinin türbinler aracılığıyla kinetik enerjiye dönüştürülmesiyle meydana gelmektedir. Yenilenebilir bir enerji olan osmotik enerjiye en uygun doğal alanl...
Investigation of Porosity and Permeability Impairment in Sandstones by X-ray Analysis and Simulation Iscan, A. G.; Kök, Mustafa Verşan; Civan, F. (Informa UK Limited, 2009-01-01) Both porosity and permeability constitute the major parameters in core analysis. In this study, the variation of these two parameters along a sandstone core sample was investigated during formation damage. A water-based drilling fluid was dynamically circulated through the core sample for three different time intervals of 15 min, 45 min, and 60 min at 100 psi circulation pressure. The core sample was analyzed using x-ray digital radiography by sectional image approach. The differences in the porous media du...
Spherical wave expansion of the time-domain free-space Dyadic Green's function Azizoglu, SA; Koç, Seyit Sencer; Buyukdura, OM (Institute of Electrical and Electronics Engineers (IEEE), 2004-03-01) The importance of expanding Green's functions, particularly free-space Green's functions in terms of orthogonal wave functions is practically self-evident when frequency domain scattering problems are of interest. With the relatively recent and widespread interest in time-domain scattering problems, similar expansions of Green's functions are expected to be useful in the time-domain. In this paper, an expression, expanded in terms of orthogonal spherical vector wave functions, for the time-domain free-space...

Citation Formats

N. Tunçbağ and A. GÜRSOY, “HotPoint: hot spot prediction server for protein interfaces,” NUCLEIC ACIDS RESEARCH, pp. 0–0, 2010, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/31892.