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Voronoiabioinformatics.charite.de/voronoiaVoronoia is a program suite for analysis and visualization of the atomic packing of protein structures. It is based on the Voronoi Cell method and can be used to estimate the quality of a protein structure, e.g. by comparing the packing density of buried atoms to a reference data set or by highlighting protein regions with large packing defects. It allows browsing of pre-calculated packing densities and cavities, and de novo calculation for single protein structures and data sets. |
PrinCCes: Continuity-based geometric decomposition and systematic visualization of the void repertoiwww.sciencedirect.com/science/article/pii/S1093326315300565PrinCCes (Protein internal Channel & Cavity estimation) is a computer program supporting the visualization of voids. It includes a novel algorithm for the decomposition of the entire void volume of the protein or protein complex to individual entities. The decomposition is based on continuity. An individual void is defined by uninterrupted extension in space: a spherical probe can freely move between any two internal locations of a continuous void. Continuous voids are detected irrespective of their topological complexity, they may contain any number of holes and bifurcations. The voids of a protein can be visualized one by one or in combinations as triangulated surfaces. The output is automatically exported to free VMD (Visual Molecular Dynamics) or Chimera software, allowing the 3D rotation of the surfaces and the production of publication quality images. PrinCCes with graphic user interface and command line versions are available for MS Windows and Linux. |
Extracting ligands from receptors by reversed targeted molecular dynamicslink.springer.com/article/10.1007/s10822-015-9863-2#/page-1Short targeted MD trajectories are used to expel ligands from binding sites. The expulsion is governed by a linear increase of the target RMSD value, growing from zero to an arbitrary chosen final RMSD that forces the ligand to a selected distance outside of the receptor. The RMSD lag (i.e., the difference between the imposed and the actual RMSD) can be used to follow barriers encountered by the ligand during its way out of the receptor. The force constant used for the targeted MD can transform the RMSD lag into a strain energy. Integration of the (time-dependent) strain energy over time yields a value with the dimensions of “action” (i.e, energy multiplied by time) and can serve as a measure for the overall effort required to extract the ligand from its binding site. |
A New Method for Navigating Optimal Direction for Pulling Ligand from Binding Pocket: Application topubs.acs.org/doi/pdf/10.1021/acs.jcim.5b00386New method for finding the optimal path for pulling a ligand from the binding pocket using steered molecular dynamics (SMD). Scoring function is defined as the steric hindrance caused by a receptor to ligand movement. Then the optimal path corresponds to the minimum of this scoring function. The new method is called MSH (Minimal Steric Hindrance). Contrary to existing navigation methods, this approach takes into account the geometry of the ligand. |
Geometric Tunnel Prediction in Cytochrome P450 Enzymesjournals.plos.org/plosone/article?id=10.1371/journal.pone.0099408The paper Ensemble Generation and the Influence of Protein Flexibility on Geometric Tunnel Prediction in Cytochrome P450 Enzymes by Kingsley and Lill presents a comparison of tunnels found in a single crystal structure with ensembles of various sizes generated using different methods on both the apo and holo forms of cytochrome P450 enzymes CYP119, CYP2C9, and CYP3A4. Several protein structure clustering methods were tested in an attempt to generate smaller ensembles that were capable of reproducing the data from larger ensembles. Ultimately, they found that by including members from both the apo and holo data sets, they could produce ensembles containing less than 15 members that were comparable to apo or holo ensembles containing over 100 members. Furthermore, they found that, in the absence of either apo or holo crystal structure data, pseudo-apo or –holo ensembles (e.g., adding ligand to apo protein throughout MD simulations) could be used to resemble the structural ensembles of the corresponding apo and holo ensembles, respectively. Their findings not only further highlight the importance of including protein flexibility in geometric tunnel prediction, but also suggest that smaller ensembles can be as capable as larger ensembles at capturing many of the protein motions important for tunnel prediction at a lower computational cost. |
Voronoi-Based Extraction and Visualization of Molecular Pathswww.ncbi.nlm.nih.gov/pubmed/22034320Another approach to the detection of molecular paths is described in paper by Lindow et al. (http://www.ncbi.nlm.nih.gov/pubmed/22034320). Using a novel filtering method, they extract the significant paths from the Voronoi diagram of spheres. For the interactive visualization of molecules and their paths, they present several methods using deferred shading and other state-of-the-art techniques. To allow for a fast overview of reachable regions of the molecule, they illuminate the molecular surface using a large number of light sources placed on the extracted paths. They also provide a method to compute the extension surface of selected paths and visualize it using the skin surface. even deeply buried paths. |
Voxel Mapshomepages.laas.fr/nic/Papers/09TCBB.pdfThe research paper available at http://homepages.laas.fr/nic/Papers/09TCBB.pdf introduces an approach to encoding molecular motions. It builds on the combination of robotic path planning algorithms and molecular modeling methods for computing large-amplitude molecular motions, and introduces voxel maps as a computational tool to encode and to represent such motions. They investigate several applications and show results that illustrate the interest of such representation. |
MoMA-LigPathmoma.laas.frMoMA-LigPath is a web server simulating protein-ligand unbinding. It is based on a mechanistic representation of the molecular system, considering partial flexibility, and on the application of a robotics-inspired algorithm to explore the conformational space. Such a purely geometric approach, together with the efficiency of the exploration algorithm, enables the simulation of ligand unbinding within very short computing time. Ligand unbinding pathways generated by MoMA-LigPath are a first approximation that can provide very useful information about protein- ligand interactions. MoMA- LigPath is available at http://moma.laas.fr. The web server is free and open to all users, with no login requirement. |
MOLEonlinencbr.muni.cz/moleMOLEonline 2.0 is an interactive web-based extension of the MOLE tool for analysis of biomacromolecular channels. For each channel, MOLEonline displays a 3D graphical representation of the channel, its profile accompanied by a list of lining residues and also its basic physicochemical properties. The MOLEonline 2.0 application is freely available via the Internet at http://ncbr.muni.cz/mole or http://mole.upol.cz |
CHEXVISvgl.serc.iisc.ernet.in/chexvis/CHEXVIS is a tool for molecular chunnel extraction and visualization. It is based on the alpha complex representation. The method computes geometrically feasible channels, stores both the volume occupied by the channel and its centerline in a unified representation, and reports significant channels. The representation also supports efficient computation of channel profiles that help understand channel properties. They also describe methods for effective visualization of the channels and their profiles. |
HOLLOWhollow.sourceforge.netHOLLOW is a tool for generating accurate representations of channel and interior surfaces in molecular structures. The program generates a "casting" of the interior volume of the protein as dummy atoms. They show that the molecular surface of the dummy atoms closely approximates the channel surface, where this complementary surface of the protein channel can be displayed without superfluous surfaces. HOLLOW is written in PYTHON and is available at http://hollow.sourceforge.net. |
BetaCavityWebvoronoi.hanyang.ac.kr/betacavityweb/BetaCavityWeb is a webserver which computes cavities for a given molecular structure and a given spherical probe, and reports their geometrical properties: volume, boundary area, buried area, etc. The server’s algorithms are based on the Voronoi diagram of atoms and its derivative construct: the betacomplex. The correctness of the computed result and computational efficiency are both mathematically guaranteed. BetaCavityWeb is freely accessible at the Voronoi Diagram Research Center (VDRC)(http://voronoi.hanyang.ac.kr/betacavityweb). |
VMDwww.ks.uiuc.edu/Research/vmdVMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. |
CASTpsts-fw.bioengr.uic.edu/castp/calculation.phpCASTp is a program for identification and measurements of surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules. It measures analytically the area and volume of each pocket and cavity, both in solvent accessible surface (SA, Richards' surface) and molecular surface (MS, Connolly's surface). It also measures the number of mouth openings, area of the openings, circumference of mouth lips, in both SA and MS surfaces for each pocket. |
VOIDOOxray.bmc.uu.se/usf/voidoo.htmlVOIDOO is a program for detection of cavities in macromolecular structures. It uses an algorithm that makes it possible to detect even certain types of cavities that are connected to "the outside world". Three different types of cavity can be handled by VOIDOO: Van der Waals cavities (the complement of the molecular van der Waals surface), probe-accessible cavities (the cavity volume that can be occupied by the centres of probe atoms) and MS-like probe-occupied cavities (the volume that can be occupied by probe atoms, i.e. including their radii). |
SLITHERbioinfo.mc.ntu.edu.tw/slither/SLITHER is a web server for generating contiguous conformations of substrate molecules entering into deep active sites of proteins or migrating across membrane transporters. It adopts an iterative docking scheme, which combines with a puddle-skimming procedure, i.e., repeatedly elevating the potential energies of the identified global minima and determines the contiguous binding modes of substrates inside the protein. SLITHER can be applied to predict whether a substrate molecule can crawl through an inner channel or a half-channel of proteins across surmountable energy barriers. It is available at http://bioinfo.mc.ntu.edu.tw/slither/or http://slither.rcas.sinica.edu.tw/. |
Q-SiteFinderwww.modelling.leeds.ac.uk/qsitefinderQ-SiteFinder is an energy-based method for the prediction of protein-ligand binding sites. It uses the interaction energy between the protein and a simple van der Waals probe to locate energetically favourable binding sites. Energetically favourable probe sites are clustered according to their spatial proximity and clusters are then ranked according to the sum of interaction energies for sites within each cluster. A pocket detection algorithm based on Ligsite written to compare pocket detection with Q-Site Finder. |
Qhullwww.qhull.orgQhull program computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. It handles roundoff errors from floating point arithmetic. It computes volumes, surface areas, and approximations to the convex hull. |
PoreWalkerwww.ebi.ac.uk/thornton-srv/software/PoreWalkerPoreWalker is a fully automated method which detects and fully characterises channels in transmembrane proteins from their 3D structures. A stepwise procedure is followed in which the pore centre and pore axis are first identified and optimised using geometric criteria, and then the biggest and longest cavity through the channel is detected. |
PyMOLwww.pymol.orgPyMOL is a user-sponsored molecular visualization system on an open-source foundation. PyMOL is a powerful and comprehensive molecular visualization product for rendering and animating 3D molecular structures. |
PASSwww.ccl.net/cca/software/UNIX/pass/overview.shtmlPASS is a simple computational tool that uses geometry to characterize regions of buried volume in proteins and to identify positions likely to represent binding sites based upon the size, shape, and burial extent of these volumes. PASS'S utility as a predictive tool for binding site identification is tested by predicting known binding sites of proteins in the PDB using both complexed macromolecules and their corresponding apo-protein structures. |
Molemole.chemi.muni.cz/web/index.phpMole is a program for rapid and fully automated location and characterization of channels and pores in molecular structures. The core of MOLE algorithm is a Dijsktra path search algorithm, which is applied to a Voronoi mesh. |
MolAxisbioinfo3d.cs.tau.ac.il/MolAxis/molaxis.htmlMolAxis tool enables the identification of high clearance pathways or corridors which represent molecular channels in the complement space of proteins. It is extremely efficient because it samples the medial axis of the complement of the molecule, reducing the problem dimension to two, since the medial axis is composed of surface patches. It is designed to analyze proteins channels, calculate pore dimensions and analyze atom accessibility. MolAxis reads files in the standard Protein Data Bank format (PDB) containing a single frame or multiple frames generated by molecular dynamics (MD) simulations. |
HotSpot Wizardloschmidt.chemi.muni.cz/hotspotwizardHotSpot Wizard is a tool for automatic identification of hot spot sites for rational engineering of substrate specificity, activity or enantioselectivity of enzymes. HotSpot Wizard integrates selected bioinformatics databases and tools and represents an easy way to perform several structural and evolutionary analyses at once. Minimal demands on users make this server potentially useful for experimentalists with no prior knowledge of computer modelling or rational protein design. |
CHUNNELcrystal.med.upenn.edu/software.htmlCHUNNEL is an algorithm for automated identification, characterization and display of tunnels or pores in proteins. It can find and characterize tunnels with no a priori guidance or clues about the location of the tunnel mouth, and is able to find multiple tunnels if present. |
