Offers users a wide range of options for Protein Data Bank (PDB) file conversion, modification and parameterization. PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format. The PDB2PQR web service is driven by a modular, Python-based collection of routines, which provides considerable flexibility to the software and permits noninteractive, high-throughput usage.
Predicts DNA-binding proteins. PSS-DWT is based on a 1040-dimension feature vector. It is implemented in a support vector machine (SVM) classifier. This tool was employed to extract sequence features from six physicochemical properties. It employs position specific scoring matrix (PSSM) to proceed. The quality of the predictor was evaluated with the Jackknife test.
Determines topology of templates and models. GapRepairer is a server designed to deliver topological assessment of refined structure. It provides intuitive visualization of structures and entanglement for generated models. It also includes a database that contains more than 100 reconstructed structures chosen due to their unusual topology. It also enables users to model proteins without restriction on number of the gaps.
Serves for computation of root mean square deviations (RMSD). RapidRMSD consists of an algorithm that determines an exact set of RMSDs corresponding to flexible molecular motions in constant time with respect to the number of atoms in the molecule instead of quadratic time. This program can be useful for flexible docking applications and for high-throughput analyses of modeling and simulation results.
Treats polarization effects in various chemical and physical environments, using permanent electrostatic multipole moments through the quadrupole at each atom. AMOEBA uses an interactive atomic dipole induction scheme where the field produced by permanent multipoles and induced dipoles induces a dipole at each polarizable site, and each such induced dipole then further polarizes other atoms. AMOEBA is a part of the complete package TINKER.
Examines the ligand-free protein structure and predicts the conserved or displaced status of its water molecules upon ligand binding. Consolv uses an algorithm coupling a k-nearest-neighbors classifier (knn) with a genetic algorithm. The software can train on additional protein structures and test other environmental features of water molecules’ environments for their ability to improve discrimination between conserved and displaced water sites.
Provides a neural network model for predicting cis-isomers. SPOT-Omega was developed to predict both imide and amide bonds. It was developed to be useful for assisting function prediction but also for protein structure prediction as well. This method utilizes two evolutionary profiles: physicochemical representations of the amino acid residues, and the outputs of predicted 1D structural properties as its inputs.
Computes phase probability distributions for SAD data. SOLVE/RESOLVE can be used for the recognition of NCS, density modification, and automated model-building. It determines the occupancies and positions of the anomalously-scattering atoms. This tool employs a library of side chain templates to match side chain density in a map with side chain types and rotamers in a probabilistic fashion.
Discovers DNA-binding proteins. PSSM-DCT is based on a 100-dimension feature vector. It was used to extract sequence features from six physicochemical properties. This tool performs Discrete Wavelet Transform (DWT) and employs position specific scoring matrix (PSSM) to proceed. Its predictive performance for different parameters was tested via a five-fold cross validation. The quality of the predictor was evaluated using the Jackknife test.
Assists users in evaluating and choosing a pairwise alignment algorithm. EPAA is an algorithm that is based on the construction of a distance matrix coupled to a k-means method for algorithms performances’ measurements. The method generates two plots: one including original family labels and one with the clusters. It can be used to evaluate alignment quality as well as for deducing evolutionary relationships from clusters.
Visualizes protein structures DNA/RNA sequences into a virtual reality (VR) environment. BioVR proposes a platform usable through Oculus Rift intending to facilitate an interactive browsing of genomic variants. The application aims to assists users in highlighting sequence-structure relationship of important residues of a protein. It was tested on a representation of the Gria2 gene of Rattus norvegicus.
Provides a tool for optimal data-driven parameterization of coiled coils (CC). CCParams offers several different features such as parameterization of an a-helix, generation of an extended parameterisation vector for every CC fragment in order to preparing the dataset for principal component analysis (PCA), extraction of 15-residue CC fragments or interactive visualization of the CC parameters in the module PyMOL.
Determines hydrogen bond inter-molecular distances and distance to surface from PDB files. HydrogenBondifier contains basic functions for structure information and a scriptable interface to pymol. It can be useful in the context of hydrogen exchange experiments.
Calculates and applies the inner distances for 3D volumetric shapes with a visibility graph. VMID is based on the visibility graph approach with a clustering technique that computes directly on the volumetric model without any surface reconstruction procedure. This software uses the inner distance for shape description via the common properties shared with known extrinsic shape descriptors. Inner distance can approximate complex shapes and avoid the problem of articulated deformation.
Determines the oligomeric states directly from the protein sequence of a large set of fluorescent proteins (FPs) compiled from the literature. osFP employs the decision tree (DT) approach to classify FPs as being either monomeric or oligomeric. It provides six classes of sequence descriptors consisting of acid/dipeptide/tripeptide composition (AAC/ DPC/TPC), autocorrelation (AC), composition, transition and distribution (CTD), conjoint triad (Ctriad), quasi-sequence-order (QSO) and pseudo-amino acid composition (PseAAC).