共 26 条
HotPoint: hot spot prediction server for protein interfaces
被引:147
作者:

Tuncbag, Nurcan
论文数: 0 引用数: 0
h-index: 0
机构: Koc Univ, Ctr Computat Biol & Bioinformat, TR-34450 Sariyer, Turkey

Keskin, Ozlem
论文数: 0 引用数: 0
h-index: 0
机构:
Koc Univ, Ctr Computat Biol & Bioinformat, TR-34450 Sariyer, Turkey Koc Univ, Ctr Computat Biol & Bioinformat, TR-34450 Sariyer, Turkey

Gursoy, Attila
论文数: 0 引用数: 0
h-index: 0
机构: Koc Univ, Ctr Computat Biol & Bioinformat, TR-34450 Sariyer, Turkey
机构:
[1] Koc Univ, Ctr Computat Biol & Bioinformat, TR-34450 Sariyer, Turkey
关键词:
BINDING-ENERGY;
RECEPTOR;
DATABASE;
D O I:
10.1093/nar/gkq323
中图分类号:
Q5 [生物化学];
Q7 [分子生物学];
学科分类号:
071010 ;
081704 ;
摘要:
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.
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收藏
页码:W402 / W406
页数:5
相关论文
共 26 条
[1]
PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces
[J].
Assi, Salam A.
;
Tanaka, Tomoyuki
;
Rabbitts, Terence H.
;
Fernandez-Fuentes, Narcis
.
NUCLEIC ACIDS RESEARCH,
2010, 38 (06)
:e86.1-e86.11

Assi, Salam A.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Leeds, Leeds Inst Mol Med, Sect Expt Therapeut, St Jamess Univ Hosp, Leeds LS9 7TF, W Yorkshire, England Univ Leeds, Leeds Inst Mol Med, Sect Expt Therapeut, St Jamess Univ Hosp, Leeds LS9 7TF, W Yorkshire, England

Tanaka, Tomoyuki
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Leeds, Leeds Inst Mol Med, Sect Expt Therapeut, St Jamess Univ Hosp, Leeds LS9 7TF, W Yorkshire, England Univ Leeds, Leeds Inst Mol Med, Sect Expt Therapeut, St Jamess Univ Hosp, Leeds LS9 7TF, W Yorkshire, England

Rabbitts, Terence H.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Leeds, Leeds Inst Mol Med, Sect Expt Therapeut, St Jamess Univ Hosp, Leeds LS9 7TF, W Yorkshire, England Univ Leeds, Leeds Inst Mol Med, Sect Expt Therapeut, St Jamess Univ Hosp, Leeds LS9 7TF, W Yorkshire, England

Fernandez-Fuentes, Narcis
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Leeds, Leeds Inst Mol Med, Sect Expt Therapeut, St Jamess Univ Hosp, Leeds LS9 7TF, W Yorkshire, England Univ Leeds, Leeds Inst Mol Med, Sect Expt Therapeut, St Jamess Univ Hosp, Leeds LS9 7TF, W Yorkshire, England
[2]
Anatomy of hot spots in protein interfaces
[J].
Bogan, AA
;
Thorn, KS
.
JOURNAL OF MOLECULAR BIOLOGY,
1998, 280 (01)
:1-9

Bogan, AA
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Calif San Francisco, Grad Grp Biophys, San Francisco, CA 94143 USA Univ Calif San Francisco, Grad Grp Biophys, San Francisco, CA 94143 USA

Thorn, KS
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Calif San Francisco, Grad Grp Biophys, San Francisco, CA 94143 USA Univ Calif San Francisco, Grad Grp Biophys, San Francisco, CA 94143 USA
[3]
A feature-based approach to modeling proteinprotein interaction hot spots
[J].
Cho, Kyu-il
;
Kim, Dongsup
;
Lee, Doheon
.
NUCLEIC ACIDS RESEARCH,
2009, 37 (08)
:2672-2687

Cho, Kyu-il
论文数: 0 引用数: 0
h-index: 0
机构:
Korea Adv Inst Sci & Technol, Dept Bio & Brain Engn, Taejon 305701, South Korea Korea Adv Inst Sci & Technol, Dept Bio & Brain Engn, Taejon 305701, South Korea

Kim, Dongsup
论文数: 0 引用数: 0
h-index: 0
机构:
Korea Adv Inst Sci & Technol, Dept Bio & Brain Engn, Taejon 305701, South Korea Korea Adv Inst Sci & Technol, Dept Bio & Brain Engn, Taejon 305701, South Korea

Lee, Doheon
论文数: 0 引用数: 0
h-index: 0
机构:
Korea Adv Inst Sci & Technol, Dept Bio & Brain Engn, Taejon 305701, South Korea Korea Adv Inst Sci & Technol, Dept Bio & Brain Engn, Taejon 305701, South Korea
[4]
A HOT-SPOT OF BINDING-ENERGY IN A HORMONE-RECEPTOR INTERFACE
[J].
CLACKSON, T
;
WELLS, JA
.
SCIENCE,
1995, 267 (5196)
:383-386

CLACKSON, T
论文数: 0 引用数: 0
h-index: 0
机构:
GENENTECH INC, DEPT PROT ENGN, S SAN FRANCISCO, CA 94080 USA GENENTECH INC, DEPT PROT ENGN, S SAN FRANCISCO, CA 94080 USA

WELLS, JA
论文数: 0 引用数: 0
h-index: 0
机构:
GENENTECH INC, DEPT PROT ENGN, S SAN FRANCISCO, CA 94080 USA GENENTECH INC, DEPT PROT ENGN, S SAN FRANCISCO, CA 94080 USA
[5]
KFC Server: interactive forecasting of protein interaction hot spots
[J].
Darnell, Steven J.
;
LeGault, Laura
;
Mitchell, Julie C.
.
NUCLEIC ACIDS RESEARCH,
2008, 36
:W265-W269

Darnell, Steven J.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA

LeGault, Laura
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Wisconsin, Dept Comp Sci, Madison, WI 53706 USA Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA

Mitchell, Julie C.
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA
Univ Wisconsin, Dept Math, Madison, WI 53706 USA Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA
[6]
An automated decision-tree approach to predicting protein interaction hot spots
[J].
Darnell, Steven J.
;
Page, David
;
Mitchell, Julie C.
.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,
2007, 68 (04)
:813-823

Darnell, Steven J.
论文数: 0 引用数: 0
h-index: 0
机构: Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA

Page, David
论文数: 0 引用数: 0
h-index: 0
机构: Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA

Mitchell, Julie C.
论文数: 0 引用数: 0
h-index: 0
机构: Univ Wisconsin, Dept Biochem, Madison, WI 53706 USA
[7]
The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces
[J].
Fischer, TB
;
Arunachalam, KV
;
Bailey, D
;
Mangual, V
;
Bakhru, S
;
Russo, R
;
Huang, D
;
Paczkowski, M
;
Lalchandani, V
;
Ramachandra, C
;
Ellison, B
;
Galer, S
;
Shapley, J
;
Fuentes, E
;
Tsai, J
.
BIOINFORMATICS,
2003, 19 (11)
:1453-1454

Fischer, TB
论文数: 0 引用数: 0
h-index: 0
机构:
Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA

Arunachalam, KV
论文数: 0 引用数: 0
h-index: 0
机构:
Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA

Bailey, D
论文数: 0 引用数: 0
h-index: 0
机构:
Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA

Mangual, V
论文数: 0 引用数: 0
h-index: 0
机构:
Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA

Bakhru, S
论文数: 0 引用数: 0
h-index: 0
机构:
Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA

Russo, R
论文数: 0 引用数: 0
h-index: 0
机构:
Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA

Huang, D
论文数: 0 引用数: 0
h-index: 0
机构:
Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA

Paczkowski, M
论文数: 0 引用数: 0
h-index: 0
机构:
Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA

Lalchandani, V
论文数: 0 引用数: 0
h-index: 0
机构:
Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA

Ramachandra, C
论文数: 0 引用数: 0
h-index: 0
机构:
Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA

Ellison, B
论文数: 0 引用数: 0
h-index: 0
机构:
Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA

Galer, S
论文数: 0 引用数: 0
h-index: 0
机构:
Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA

Shapley, J
论文数: 0 引用数: 0
h-index: 0
机构:
Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA

Fuentes, E
论文数: 0 引用数: 0
h-index: 0
机构:
Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA

Tsai, J
论文数: 0 引用数: 0
h-index: 0
机构:
Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA Texas A&M Univ, Dept Biochem & Biophys, College Stn, TX 77843 USA
[8]
Targeting protein-protein interactions with small molecules:: Challenges and perspectives for computational binding epitope detection and ligand finding
[J].
Gonzalez-Ruiz, Domingo
;
Gohlke, Holger
.
CURRENT MEDICINAL CHEMISTRY,
2006, 13 (22)
:2607-2625

Gonzalez-Ruiz, Domingo
论文数: 0 引用数: 0
h-index: 0
机构:
Goethe Univ Frankfurt, Dept Biol Sci, D-6000 Frankfurt, Germany Goethe Univ Frankfurt, Dept Biol Sci, D-6000 Frankfurt, Germany

Gohlke, Holger
论文数: 0 引用数: 0
h-index: 0
机构:
Goethe Univ Frankfurt, Dept Biol Sci, D-6000 Frankfurt, Germany Goethe Univ Frankfurt, Dept Biol Sci, D-6000 Frankfurt, Germany
[9]
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
[J].
Guerois, R
;
Nielsen, JE
;
Serrano, L
.
JOURNAL OF MOLECULAR BIOLOGY,
2002, 320 (02)
:369-387

Guerois, R
论文数: 0 引用数: 0
h-index: 0
机构: EMBL, D-69117 Heidelberg, Germany

Nielsen, JE
论文数: 0 引用数: 0
h-index: 0
机构: EMBL, D-69117 Heidelberg, Germany

Serrano, L
论文数: 0 引用数: 0
h-index: 0
机构: EMBL, D-69117 Heidelberg, Germany
[10]
Empirical estimation of the energetic contribution of individual interface residues in structures of protein-protein complexes
[J].
Guharoy, Mainak
;
Chakrabarti, Pinak
.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN,
2009, 23 (09)
:645-654

Guharoy, Mainak
论文数: 0 引用数: 0
h-index: 0
机构:
Bose Inst, Dept Biochem, Kolkata 700054, W Bengal, India Bose Inst, Dept Biochem, Kolkata 700054, W Bengal, India

Chakrabarti, Pinak
论文数: 0 引用数: 0
h-index: 0
机构:
Bose Inst, Dept Biochem, Kolkata 700054, W Bengal, India Bose Inst, Dept Biochem, Kolkata 700054, W Bengal, India