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Solvent accessibility detection software tools | Protein structure data analysis

Accurate prediction of relative solvent accessibilities (RSAs) of amino acid residues in proteins may be used to facilitate protein structure prediction and functional annotation.Source text:(Wang and Hu 2015) Accurate prediction of nuclear…
SPINE-X
Desktop

SPINE-X

Allows prediction of secondary structure, accessible surface area and dihedral…

Allows prediction of secondary structure, accessible surface area and dihedral angles. SPINE-X is a secondary structure prediction method consisting of six steps of iterative prediction of secondary…

PSpro
Desktop

PSpro

Allows users to forecast protein secondary structure (SS). PSpro is also…

Allows users to forecast protein secondary structure (SS). PSpro is also efficient in predicting residue-residue contacts, contact map and solvent accessibility.

NetSurfP
Web

NetSurfP

Predicts the relative surface accessibility of an amino acid and simultaneously…

Predicts the relative surface accessibility of an amino acid and simultaneously predicts the reliability for each prediction, in the form of a Z-score. NetSurfP is composed of two neural network…

MUPRED
Web

MUPRED

Allows prediction of the three-dimensional structure of a protein. MUPRED uses…

Allows prediction of the three-dimensional structure of a protein. MUPRED uses both structural information and sequence profile information to realize this process. This tool first estimates the…

PredRSA
Algorithm

PredRSA Prediction of Relative Solvent Accessible surface area

Predicts relative solvent accessible surface area (RSA) of residues. PredRSA…

Predicts relative solvent accessible surface area (RSA) of residues. PredRSA integrates gradient boosted regression trees (GBRT) algorithm with multiple sequence-based features and a global…

PCASA
Desktop

PCASA Protein-Ca Solvent Accessibilities

Predicts residue-wise Solvent Accessible Area (SASAs) from Ca coordinates of…

Predicts residue-wise Solvent Accessible Area (SASAs) from Ca coordinates of protein structures. PCASA is method that finds utility in accounting for solvation effects in coarse-grained protein…

ASAquick
Desktop

ASAquick

Provides a quick accessible surface area predictor. ASAquick is an algorithm…

Provides a quick accessible surface area predictor. ASAquick is an algorithm constructed out of several subroutines that process the data, initialize the model, and train it. It is also capable of…

SABLE
Web
Desktop

SABLE Solvent AccessiBiLitiEs

A regression-based method for secondary structure prediction that utilizes…

A regression-based method for secondary structure prediction that utilizes predicted solvent exposure of an amino acid residue as an additional attribute describing its environment. SABLE follows the…

RSARF
Desktop
Ermod
Desktop

Ermod

Allows users to calculate the solvation free energy to arbitrary solvents,…

Allows users to calculate the solvation free energy to arbitrary solvents, including inhomogeneous systems, and can run in cooperation with state-of-art molecular simulation softwares, such as NAMD,…

AcconPred
Desktop

AcconPred

A method for predicting solvent accessibility and contact number…

A method for predicting solvent accessibility and contact number simultaneously, which is based on a shared weight multitask learning framework under the CNF (conditional neural fields) model. The…

RVP-NET
Web

RVP-NET

Predicts the real values of solvent accessibility in a protein using a neural…

Predicts the real values of solvent accessibility in a protein using a neural network algorithm. In RVP-NET, single residue information of neighbours is used for making prediction of solvent…

NETASA
Web

NETASA

Predicts solvent accessibility of amino acids using an optimized neural network…

Predicts solvent accessibility of amino acids using an optimized neural network algorithm. NETASA provides accuracy values, which are comparable or better than other methods of ASA (accessible…

Sann
Web
Desktop

Sann Solvent Accessibility prediction by Nearest Neighbor method

Predicts the discrete state (two and three states) as well as continuous value…

Predicts the discrete state (two and three states) as well as continuous value of the solvent accessibility of a target residue. The method is based on a k-nearest neighbor method combined with…

Naccess
Desktop

Naccess

Calculates the atomic accessible surface defined by rolling a probe of given…

Calculates the atomic accessible surface defined by rolling a probe of given size around a van der Waals surface. Naccess is able to calculate the atomic and residue accessibilities for both proteins…

BioLuminate
Desktop

BioLuminate

Provides a comprehensive modeling solution for biologics. BioLuminate is a user…

Provides a comprehensive modeling solution for biologics. BioLuminate is a user interface and the kynchpin product of the Biologics Suite that is designed from the ground up, with significant user…

BMRSA
Desktop

BMRSA

Predicts protein relative solvent accessibility (RSA) from the amino acid…

Predicts protein relative solvent accessibility (RSA) from the amino acid sequence. BMRSA is a balanced model of RSA prediction based on a balanced training set and an optimized variable combination.

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