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Literature DB >> 12824325

CASTp: Computed Atlas of Surface Topography of proteins.

T Andrew Binkowski¹, Shapor Naghibzadeh, Jie Liang.

Abstract

Computed Atlas of Surface Topography of proteins (CASTp) provides an online resource for locating, delineating and measuring concave surface regions on three-dimensional structures of proteins. These include pockets located on protein surfaces and voids buried in the interior of proteins. The measurement includes the area and volume of pocket or void by solvent accessible surface model (Richards' surface) and by molecular surface model (Connolly's surface), all calculated analytically. CASTp can be used to study surface features and functional regions of proteins. CASTp includes a graphical user interface, flexible interactive visualization, as well as on-the-fly calculation for user uploaded structures. CASTp is updated daily and can be accessed at http://cast.engr.uic.edu.

Mesh：

Substances：
Proteins

Year: 2003 PMID： 12824325 PMCID： PMC168919 DOI： 10.1093/nar/gkg512

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

17 in total

1. Crystal structure of the quorum-sensing protein LuxS reveals a catalytic metal site.

Authors: M T Hilgers; M L Ludwig
Journal: Proc Natl Acad Sci U S A Date: 2001-09-11 Impact factor: 11.205

2. The role of electrostatic interactions in human serum albumin binding and stabilization by halothane.

Authors: Renyu Liu; Ravindernath Pidikiti; Chung-Eun Ha; Charles E Petersen; Nadhipuram V Bhagavan; Roderic G Eckenhoff
Journal: J Biol Chem Date: 2002-07-12 Impact factor: 5.157

3. Common protein architecture and binding sites in proteases utilizing a Ser/Lys dyad mechanism.

Authors: M Paetzel; N C Strynadka
Journal: Protein Sci Date: 1999-11 Impact factor: 6.725

4. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design.

Authors: J Liang; H Edelsbrunner; C Woodward
Journal: Protein Sci Date: 1998-09 Impact factor: 6.725

5. Protein clefts in molecular recognition and function.

Authors: R A Laskowski; N M Luscombe; M B Swindells; J M Thornton
Journal: Protein Sci Date: 1996-12 Impact factor: 6.725

Review 6. Liver fatty acid binding protein: species variation and the accommodation of different ligands.

Authors: J Thompson; A Reese-Wagoner; L Banaszak
Journal: Biochim Biophys Acta Date: 1999-11-23

7. Kinemages--simple macromolecular graphics for interactive teaching and publication.

Authors: D C Richardson; J S Richardson
Journal: Trends Biochem Sci Date: 1994-03 Impact factor: 13.807

8. Studies of the ligand binding reaction of adipocyte lipid binding protein using the fluorescent probe 1, 8-anilinonaphthalene-8-sulfonate.

Authors: J J Ory; L J Banaszak
Journal: Biophys J Date: 1999-08 Impact factor: 4.033

9. Crystal structures of zinc-free and -bound heme domain of human inducible nitric-oxide synthase. Implications for dimer stability and comparison with endothelial nitric-oxide synthase.

Authors: H Li; C S Raman; C B Glaser; E Blasko; T A Young; J F Parkinson; M Whitlow; T L Poulos
Journal: J Biol Chem Date: 1999-07-23 Impact factor: 5.157

10. Lipid-protein interactions in lipovitellin.

Authors: James R Thompson; Leonard J Banaszak
Journal: Biochemistry Date: 2002-07-30 Impact factor: 3.162

193 in total

1. pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins.

Authors: T Andrew Binkowski; Patrick Freeman; Jie Liang
Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971

2. An antibody as surrogate receptor reveals determinants of activity of an innate immune peptide antibiotic.

Authors: Suvendu Lomash; Sushma Nagpal; Dinakar M Salunke
Journal: J Biol Chem Date: 2010-09-13 Impact factor: 5.157

3. Structure-function perturbation and dissociation of tetrameric urate oxidase by high hydrostatic pressure.

Authors: Eric Girard; Stéphane Marchal; Javier Perez; Stéphanie Finet; Richard Kahn; Roger Fourme; Guillaume Marassio; Anne-Claire Dhaussy; Thierry Prangé; Marion Giffard; Fabienne Dulin; Françoise Bonneté; Reinhard Lange; Jacques H Abraini; Mohamed Mezouar; Nathalie Colloc'h
Journal: Biophys J Date: 2010-05-19 Impact factor: 4.033

CASTp: Computed Atlas of Surface Topography of proteins.

1. Crystal structure of the quorum-sensing protein LuxS reveals a catalytic metal site.

2. The role of electrostatic interactions in human serum albumin binding and stabilization by halothane.

3. Common protein architecture and binding sites in proteases utilizing a Ser/Lys dyad mechanism.

4. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design.

5. Protein clefts in molecular recognition and function.

Review 6. Liver fatty acid binding protein: species variation and the accommodation of different ligands.

7. Kinemages--simple macromolecular graphics for interactive teaching and publication.

8. Studies of the ligand binding reaction of adipocyte lipid binding protein using the fluorescent probe 1, 8-anilinonaphthalene-8-sulfonate.

9. Crystal structures of zinc-free and -bound heme domain of human inducible nitric-oxide synthase. Implications for dimer stability and comparison with endothelial nitric-oxide synthase.

10. Lipid-protein interactions in lipovitellin.

1. pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins.

2. An antibody as surrogate receptor reveals determinants of activity of an innate immune peptide antibiotic.

3. Structure-function perturbation and dissociation of tetrameric urate oxidase by high hydrostatic pressure.

4. 1.6 A crystal structure of YteR protein from Bacillus subtilis, a predicted lyase.

5. Protein surface analysis for function annotation in high-throughput structural genomics pipeline.

6. Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses.

7. Solution structure of inhibitor-free human metalloelastase (MMP-12) indicates an internal conformational adjustment.

8. On quantification of geometry and topology of protein pockets and channels for assessing mutation effects.

9. Crystal Structures of the Nuclear Receptor, Liver Receptor Homolog 1, Bound to Synthetic Agonists.

10. On the role of physics and evolution in dictating protein structure and function.