Residue depth
Encyclopedia
Residue depth is a solvent exposure
measure that describes to what extent a residue
is buried in the protein structure
space. It complements the information provided by conventional accessible surface area
(ASA).
Currently, predictions in regards to whether a residue is exposed or buried are used in a wide variety of protein structure prediction engines. Such prediction can provide valuable information for protein fold
recognition, functional residue
prediction and protein drug design
.
To date several approaches have been proposed to predict RD values from protein sequences. Yuan and Wang proposed a computational framework that uses sequential evolutionary information contained in PSI-BLAST profiles and the global protein size information to quantify the relationship between RD and protein sequence. Zhang et al. proposed the RDpred method to predict RD values based on predicted secondary structure
, residue position and PSI-BLAST profile. More recently, Song et al. described another sequence-based method that also uses support vector regression to quantify the RD-sequence relationship. Their webserver Prodepth, is developed to facilitate RD prediction analysis for sequences submitted by interested users. In addition, Prodepth server can predict the solvent-accessible surface area (ASA) value for each residue for users' submitted sequence. Based on the predicted ASA and RD values, it will further output the two-state solvent accessibility prediction by classifying a residue as being exposed or buried. Prodepth server is available at http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/Prodepth/ .
Solvent exposure
The solvent exposure of an amino acid in a protein measures to what extent theamino acid is accessible to the solvent surrounding the protein. Generally speaking, hydrophobic amino acids will be buried inside the protein and thus shielded from the solvent, while hydrophilic amino acids will be...
measure that describes to what extent a residue
Residue
Residue may refer to:* Residue , material remaining after a distillation or an evaporation, or portion of a larger molecule** In particular, in biology, often refers specifically to an amino acid...
is buried in the protein structure
Protein structure
Proteins are an important class of biological macromolecules present in all organisms. Proteins are polymers of amino acids. Classified by their physical size, proteins are nanoparticles . Each protein polymer – also known as a polypeptide – consists of a sequence formed from 20 possible L-α-amino...
space. It complements the information provided by conventional accessible surface area
Accessible surface area
The accessible surface area is the surface area of a biomolecule that is accessible to a solvent. The ASA is usually quoted in square ångstrom . ASA was first described by Lee & Richards in 1971 and is sometimes called the Lee-Richards molecular surface...
(ASA).
Currently, predictions in regards to whether a residue is exposed or buried are used in a wide variety of protein structure prediction engines. Such prediction can provide valuable information for protein fold
Protein folding
Protein folding is the process by which a protein structure assumes its functional shape or conformation. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil....
recognition, functional residue
Functional residual capacity
Functional Residual Capacity is the volume of air present in the lungs, specifically the parenchyma tissues, at the end of passive expiration...
prediction and protein drug design
Drug design
Drug design, also sometimes referred to as rational drug design or structure-based drug design, is the inventive process of finding new medications based on the knowledge of the biological target...
.
To date several approaches have been proposed to predict RD values from protein sequences. Yuan and Wang proposed a computational framework that uses sequential evolutionary information contained in PSI-BLAST profiles and the global protein size information to quantify the relationship between RD and protein sequence. Zhang et al. proposed the RDpred method to predict RD values based on predicted secondary structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
, residue position and PSI-BLAST profile. More recently, Song et al. described another sequence-based method that also uses support vector regression to quantify the RD-sequence relationship. Their webserver Prodepth, is developed to facilitate RD prediction analysis for sequences submitted by interested users. In addition, Prodepth server can predict the solvent-accessible surface area (ASA) value for each residue for users' submitted sequence. Based on the predicted ASA and RD values, it will further output the two-state solvent accessibility prediction by classifying a residue as being exposed or buried. Prodepth server is available at http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/Prodepth/ .