INTERCAAT: identifying interface residues between macromolecules

2021 ◽  
Author(s):  
Steven Grudman ◽  
J Eduardo Fajardo ◽  
Andras Fiser
Keyword(s):  
Voronoi Tessellation ◽  
Source Code ◽  
Solvent Molecule ◽  
Three Dimensional ◽  
Supplementary Information ◽  
Dimensional Structure ◽  
Atomic Interactions ◽  
Interface Contact ◽  
Interacting Atoms ◽  
Van Der Waals Radii

Abstract Summary The Interface Contact definition with Adaptable Atom Types (INTERCAAT) was developed to determine the atomic interactions between molecules that form a known three dimensional structure. First, INTERCAAT creates a Voronoi tessellation where each atom acts as a seed. Interactions are defined by atoms that share a hyperplane and whose distance is less than the sum of each atoms’ Van der Waals radii plus the diameter of a solvent molecule. Interacting atoms are then classified and interactions are filtered based on compatibility. INTERCAAT implements an adaptive atom classification method; therefore, it can explore interfaces between a variety macromolecules. Availability and implementation Source code is freely available at: https://gitlab.com/fiserlab.org/intercaat. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Crystal structure ofL-tryptophan–fumaric acid–water (1/1/1)

2015 ◽  
Vol 71 (9) ◽  
pp. o661-o662 ◽  
Author(s):  
M. Lydia Caroline ◽  
S. Kumaresan ◽  
P. G. Aravindan ◽  
M. Peer Mohamed ◽  
G. Mani
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Fumaric Acid ◽  
Solvent Molecule ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Acid Molecule ◽  
Water Solvent ◽  
Compound C ◽  
Tryptophan Molecule

In the title compound, C11H12N2O2·C4H4O4·H2O, the L-tryptophan molecule crystallized as a zwitterion, together with a neutral fumaric acid molecule and a water solvent molecule. In the crystal, the three components are linked by a series of N—H...O, O—H...O and C—H...O hydrogen bonds, forming slabs lying parallel to (001). The slabs are connected by O—H...O hydrogen bonds, involving inversion-related fumaric acid groups, leading to the formation of a three-dimensional structure.

scholarly journals SphereCon—a method for precise estimation of residue relative solvent accessible area from limited structural information

2020 ◽  
Vol 36 (11) ◽  
pp. 3372-3378
Author(s):  
Alexander Gress ◽  
Olga V Kalinina
Keyword(s):  
Protein Function ◽  
Structural Information ◽  
Solvent Accessibility ◽  
Three Dimensional ◽  
Structural Data ◽  
Supplementary Information ◽  
Dimensional Structure ◽  
Relative Solvent Accessibility ◽  
Precise Measure ◽  
The Impact

Abstract Motivation In proteins, solvent accessibility of individual residues is a factor contributing to their importance for protein function and stability. Hence one might wish to calculate solvent accessibility in order to predict the impact of mutations, their pathogenicity and for other biomedical applications. A direct computation of solvent accessibility is only possible if all atoms of a protein three-dimensional structure are reliably resolved. Results We present SphereCon, a new precise measure that can estimate residue relative solvent accessibility (RSA) from limited data. The measure is based on calculating the volume of intersection of a sphere with a cone cut out in the direction opposite of the residue with surrounding atoms. We propose a method for estimating the position and volume of residue atoms in cases when they are not known from the structure, or when the structural data are unreliable or missing. We show that in cases of reliable input structures, SphereCon correlates almost perfectly with the directly computed RSA, and outperforms other previously suggested indirect methods. Moreover, SphereCon is the only measure that yields accurate results when the identities of amino acids are unknown. A significant novel feature of SphereCon is that it can estimate RSA from inter-residue distance and contact matrices, without any information about the actual atom coordinates. Availability and implementation https://github.com/kalininalab/spherecon. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals ShelXle: a Qt graphical user interface forSHELXL

2011 ◽  
Vol 44 (6) ◽  
pp. 1281-1284 ◽  
Author(s):  
Christian B. Hübschle ◽  
George M. Sheldrick ◽  
Birger Dittrich
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Structure Refinement ◽  
Source Code ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Graphical Display ◽  
Acta Cryst ◽  
Strongly Coupled ◽  
Difference Density

ShelXleis a graphical user interface forSHELXL[Sheldrick, G. M. (2008).Acta Cryst.A64, 112–122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for theSHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo–Fc) maps. Special features ofShelXleinclude intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions.ShelXleis completely compatible with all features ofSHELXLand is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.

scholarly journals RADI (Reduced Alphabet Direct Information): Improving execution time for direct-coupling analysis

2018 ◽  
Author(s):  
Bernat Anton ◽  
Mireia Besalú ◽  
Oriol Fornes ◽  
Jaume Bonet ◽  
Gemma De las Cuevas ◽  
...  
Keyword(s):  
Computational Cost ◽  
Three Dimensional ◽  
Computation Time ◽  
Direct Coupling ◽  
Supplementary Information ◽  
Dimensional Structure ◽  
Coupling Analysis ◽  
Direct Information ◽  
Large Proteins ◽  
Direct Coupling Analysis

AbstractMotivationDirect-coupling analysis (DCA) for studying the coevolution of residues in proteins has been widely used to predict the three-dimensional structure of a protein from its sequence. Current algorithms for DCA, although efficient, have a high computational cost of determining Direct Information (DI) values for large proteins or domains. In this paper, we present RADI (Reduced Alphabet Direct Information), a variation of the original DCA algorithm that simplifies the computation of DI values by grouping physicochemically equivalent residues.ResultsWe have compared the first top ranking 40 pairs of DI values and their closest paired contact in 3D. The ranking is also compared with results obtained using a similar but faster approach based on Mutual Information (MI). When we simplify the number of symbols used to describe a protein sequence to 9, RADI achieves similar results as the original DCA (i.e. with the classical alphabet of 21 symbols), while reducing the computation time around 30-fold on large proteins (with length around 1000 residues) and with higher accuracy than predictions based on MI. Interestingly, the simplification produced by grouping amino acids into only two groups (polar and non-polar) is still representative of the physicochemical nature that characterizes the protein structure, having a relevant and useful predictive value, while the computation time is reduced between 100 and 2500-fold.AvailabilityRADI is available at https://github.com/structuralbioinformatics/[email protected] informationSupplementary data is available in the git repository.

scholarly journals Crystal structure of bis(μ-{2-[(5-bromo-2-oxidobenzylidene)amino]ethyl}sulfanido-κ3 N,O,S){2,2′-[(3,4-dithiahexane-1,6-diyl)bis(nitrilomethanylylidene)]bis(4-bromophenolato)-κ4 O,N,N′,O′}dicobalt(III) dimethylformamide monosolvate

2019 ◽  
Vol 75 (6) ◽  
pp. 863-866
Author(s):  
Julia A. Rusanova ◽  
Vladimir N. Kokozay ◽  
Olena Bondarenko
Keyword(s):  
Crystal Structure ◽  
Solvent Molecule ◽  
Three Dimensional ◽  
Coordination Geometry ◽  
Asymmetric Unit ◽  
Dimensional Network ◽  
Distorted Octahedral ◽  
Van Der Waals Radii ◽  
Spontaneous Oxidation

The title binuclear CoIII complex, [Co2(C9H8BrNOS)2(C18H16Br2N2O2S2)]·C3H7NO, with a Schiff base ligand formed in situ from cysteamine (2-aminoethanethiol) and 5-bromosalicylaldehyde crystallizes in the space group P21. It was found that during the synthesis the ligand undergoes spontaneous oxidation, forming the new ligand H2 L′ having an S—S bond. Thus, the asymmetric unit consists of one Co2(L)2(L′) molecule and one DMF solvent molecule. Each CoIII ion has a slightly distorted octahedral S2N2O2 coordination geometry. In the crystal, the components are linked into a three-dimensional network by several S... Br, C... Br, C—H...Br, short S...C (essentially shorter than the sum of the van der Waals radii for the atoms involved) contacts as well by weak C—H...O hydrogen bonds. The crystal studied was refined as an inversion twin.

scholarly journals MicrographCleaner: a python package for cryo-EM micrograph cleaning using deep learning

2019 ◽  
Author(s):  
Ruben Sanchez-Garcia ◽  
Joan Segura ◽  
David Maluenda ◽  
C.O.S. Sorzano ◽  
J.M. Carazo
Keyword(s):  
Deep Learning ◽  
Source Code ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Particle Analysis ◽  
Single Particle Analysis ◽  
Reconstruction Process ◽  
Different Types ◽  
Deep Learning Model ◽  
Python Package

AbstractCryo-EM Single Particle Analysis workflows require from tens of thousands of high-quality particle projections to unveil the three-dimensional structure of macromolecules. Conventional methods for automatic particle picking tend to suffer from high false-positive rates, hurdling the reconstruction process. One common cause of this problem is the presence of carbon and different types of high-contrast contaminations. In order to overcome this limitation, we have developed MicrographCleaner, a deep learning package designed to discriminate which regions of micrographs are suitable for particle picking and which are not in an automatic fashion. MicrographCleaner implements a U-net-like deep learning model trained on a manually curated dataset compiled from over five hundred micrographs. The benchmarking, carried out on about one hundred independent micrographs, shows that MicrographCleaner is a very efficient approach for micrograph preprocessing. MicrographCleaner (micrograph_cleaner_em) package is available at PyPI and Anaconda Cloud and also as a Scipion/Xmipp protocol. Source code is available at https://github.com/rsanchezgarc/micrograph_cleaner_em.

scholarly journals 1-Allyl-3′-phenyl-6′H-spiro[indoline-3,4′-isoxazolo[4′,5′:5,6]pyrido[2,3-d]pyrimidine]-2,5′,7′(8′H,9′H)-trione dimethyl sulfoxide monosolvate

IUCrData ◽  
2017 ◽  
Vol 2 (1) ◽  
Author(s):  
P. Seethalakshmi ◽  
C. Palanivel
Keyword(s):  
Hydrogen Bonds ◽  
Dimethyl Sulfoxide ◽  
Phenyl Ring ◽  
Solvent Molecule ◽  
Three Dimensional ◽  
Pyrimidine Ring ◽  
Ring System ◽  
Dimensional Structure ◽  
Boat Conformation ◽  
Compound C

In the title solvated compound, C24H17N5O4·C2H6OS, the solvent molecule, dimethyl sulfoxide, is linked to the title molecule by an N—H...O hydrogen bond. The pyridine ring adopts a twist-boat conformation. The isoxazole ring is inclined to the indoline ring system, the pyrimidine ring, and the phenyl ring by 82.31 (7), 10.41 (8) and 53.77 (10)°, respectively. There is an intramolecular C—H...π interaction present involving the phenyl ring and the indoline ring system. In the crystal, molecules are connected by two pairs of N—H...O hydrogen bonds, forming chains along theb-axis direction, and enclosingR22(8) andR22(14) ring motifs. The chains are linked by C—H...O and C—H...N hydrogen bonds and offset π–π interactions, between the pyrimidine and isoxazole rings of inversion-related molecules [centroid–centroid distance = 3.7140 (9) Å], forming a three-dimensional structure.

scholarly journals A new co-crystal dinuclear/trinuclear ZnII–ZnII/ZnII–SmIII–ZnII complex with a salen-type Schiff base ligand

2018 ◽  
Vol 74 (12) ◽  
pp. 1862-1866
Author(s):  
Mamour Sarr ◽  
Mayoro Diop ◽  
Elhadj Ibrahima Thiam ◽  
Mohamed Gaye ◽  
Aliou Hamady Barry ◽  
...  
Keyword(s):  
Nitrogen Atom ◽  
Electrostatic Interactions ◽  
Solvent Molecule ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Tetrahedral Geometry ◽  
Pyramidal Geometry ◽  
Dinuclear Unit ◽  
Square Pyramidal Geometry ◽  
Oxygen Atoms

In the pentanuclear title complex, [SmZn2(C22H18N2O4)2(NCS)2(C3H7NO)2][Zn2(C22H18N2O4)(NCS)3]·C3H7NO·0.32H2O, namely bis{μ2-6,6′-dimethoxy-2,2′-[phenylene-1,2-diylbis(nitrilomethanylylidene)]diphenolato}-1κ4 O,N,N′,O′:2κ3 O,O′,O 6;2κ3 O,O′,O 6:3κ4 O,N,N′,O′-bis(dimethylformamide-2κO)dithiocyanato-1κN,3κN-2-samarium(III)-1,3-dizinc(II) {μ2-6,6′-dimethoxy-2,2′-[phenylene-1,2-diylbis(nitrilomethanylylidene)]diphenolato-1κ4 O,N,N′,O′:2κ2 O,O′}trithiocyanato-1κN;2κ2 N,N-dizinc(II) dimethylformamide monosolvate 1.32-hydrate, a dinuclear unit and a trinuclear unit co-exist. One of the ZnII centers in the dinuclear unit as well as the two ZnII centers in the trinuclear unit are located in the inner N2O2 cavity of the ligand and are coordinated to the nitrogen atom of one thiocyanate moiety, giving rise to a square-pyramidal geometry. The second ZnII center in the dinuclear unit is coordinated to the two phenolate oxygen atoms of the ligand and to two thiocyanate groups via the nitrogen atom in a tetrahedral geometry. The SmIII ion is eight-coordinated by four phenolate O atoms from the two ligand molecules, two methoxy O atoms from the two ligand molecules and two O atoms from the DFM solvent molecule. In the dinuclear unit, the two methoxy oxygen atoms remain uncoordinated while in the trinuclear unit, for each ligand one methoxy oxygen is coordinated and the other one remains uncoordinated. In the crystal, the trinuclear cationic units and dinuclear anionic units are assembled into infinite layers. These layers are held together via electrostatic interactions, forming a three-dimensional structure. In the dinuclear unit, the C and S atoms of one of the thiocyanate groups are disordered over two sets of sites in a 0.680 (4)(4):0.320 (4) ratio.

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

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