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CHARMM36m / Chemistry at HARvard Macromolecular Mechanics 36m
Improves accuracy in generating polypeptide backbone conformational ensembles for intrinsically disordered peptides and proteins. CHARMM36m come from the all-atom additive CHARMM36, a protein force field widely used in molecular modeling and simulations. This tool was found to generate a high population of left-handed α-helix (αL), inconsistent with NMR spectroscopy and small-angle X-ray scattering (SAXS) experimental measurements. The improve version is based on a refined backbone CMAP potential8 derived from reweighting calculation and a better description of specific salt bridge interactions.
Allows protein sequence analysis. ANTHEPROT is able to interactively couple multiple alignments with secondary structure predictions. It can submit tasks on a remote server and retrieve data from a remote Web server. This tool is a complete solution for Intranet protein sequence analysis for universities, biological research institutes or biomedical companies. It permits users to integrate secondary structure predictions within multiple alignment and full interactive editing of alignments.
A web application that implements a complete workflow for user customized investigation of protein sequence-structure-dynamic relationships. Bio3D-web provides unparalleled online functionality including inter-conformer relationship mapping with principal component analysis (PCA), and quantitative comparison of predicted internal dynamics across protein families via new ensemble normal mode analysis (eNMA). Together with conventional sequence and structure analysis methods these approaches allow researchers to map the structural dynamic properties of proteins for which PDB structures are available.
A web interface to the Elastic Network Model that provides a fast and simple tool to compute, visualize and analyse low-frequency normal modes of large macro-molecules and to generate a large number of different starting models for use in MR. Due to the 'rotation-translation-block' (RTB) approximation implemented in ElNemo, there is virtually no upper limit to the size of the proteins that can be treated. Upon input of a protein structure in Protein Data Bank (PDB) format, ElNemo computes its 100 lowest-frequency modes and produces a comprehensive set of descriptive parameters and visualizations, such as the degree of collectivity of movement, residue mean square displacements, distance fluctuation maps, and the correlation between observed and normal-mode-derived atomic displacement parameters (B-factors).
Provides tools for online calculation of the normal modes of large molecules (up to 100,000 atoms) maintaining a full all-atom representation of their structures, as well as access to a number of programs that utilize these collective motions for deformation and refinement of biomolecular structures. Applications include the generation of sets of decoys with correct stereochemistry but arbitrary large amplitude movements, the quantification of the overlap between alternative conformations of a molecule, refinement of structures against experimental data, such as X-ray diffraction structure factors or Cryo-EM maps and optimization of docked complexes by modeling receptor/ligand flexibility through normal mode motions.
A web-based tool for the analysis of protein flexibility. The server incorporates powerful protocols for the coarse-grained determination of protein dynamics using different versions of Normal Mode Analysis (NMA), Brownian dynamics (BD) and Discrete Dynamics (DMD). FlexServ can also analyze user provided trajectories. The server allows a complete analysis of flexibility using a large variety of metrics, including basic geometrical analysis, B-factors, essential dynamics, stiffness analysis, collectivity measures, Lindemann's indexes, residue correlation, chain-correlations, dynamic domain determination, hinge point detections, etc. Data is presented through a web interface as plain text, 2D and 3D graphics.
CHARMM-GUI Micelle Builder
Allows users to upload a membrane protein structure or download from a database and choose one or multiple detergent types to generate a preassembled micelle around the protein. CHARMM-GUI Micelle Builder aims to build a protein/micelle complex system for molecular dynamics (MD) simulation. It can be applied to various proteins with different geometries. This tool can be used for simulation studies of various protein/micelle systems to better understand the protein structure and dynamics in micelles.
Predicts hinge movements. Given a single protein structure, HingeProt automatically divides it into the rigid parts and the hinge regions connecting them. The method employs the Elastic Network Model, which is very efficient and was validated against a large data set of proteins. The output can be used in applications such as flexible protein-protein and protein-ligand docking, flexible docking of protein structures into cryo-EM maps, and refinement of low-resolution EM structures.
P.R.E.S.S. / Protein Residue-Level Structural Statistics
Furnishes an access to the statistical data on protein residue-level structural properties. P.R.E.S.S. permits the manipulation of data such as residue-level virtual bond lengths, virtual bond angles, and virtual torsion angles. It can serve to determine the residue level structural properties of proteins which are not otherwise accessible experimentally. This tool is able to assess the correlations of the virtual bond and torsion angles and display a residue-level Ramachandran-like plot for a given structure.
Improves the accuracy of protein flexibility prediction. FLEXc incorporates sequence and evolutionary information, context-based scores, predicted secondary structures and solvent accessibility, and amino acid properties. Context-based statistical scores are derived, using the mean-field potentials approach, for describing the different preferences of protein residues in flexibility states taking into consideration their amino acid context. FLEXc will be very useful in protein modeling efficiency, mainly because the search space for finding a tertiary structure goes up superlinearly with the fraction of inaccuracy.
Uses for intuitively exploring flexible molecular shape retrieval. 3DMolNavi is a web-based retrieval and navigation tool for flexible molecular shape comparison. This tool is based on the histogram of Inner Distance Shape Signature (IDSS) for fast retrieving molecules that are similar to a query molecule, and uses dimensionality reduction to navigate the retrieved results in 2D and 3D spaces. It achieves good performance and retrieval results for different classes of flexible molecules.
An approach for predicting hinges between domains using input from two complementary analyses of noncovalent bond networks: StoneHingeP, which identifies domain-hinge-domain signatures in ProFlex constraint counting results, and StoneHingeD, which does the same for DomDecomp Gaussian network analyses. Predictions for the two methods are compared to hinges defined in the literature and by visual inspection of interpolated motions between conformations in a series of proteins. Proteins can be submitted for prediction online, and the predicted hinge locations will be mapped onto the three-dimensional structure and can be rotated in Jmol.
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