Molecular Graphics: Bridging Structural Biologists and Computer Scientists
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59 BASIC BIOLOGICAL SCIENCES↗
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Results for “molecular graphics”
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Likelihood-based interactive local docking into cryo-EM maps in ChimeraX
The interpretation of cryo-EM maps often includes the docking of known or predicted structures of the components, which is particularly useful when the map resolution is worse than 4 Å. Although it can be effective to search the entire map to find the best placement of a component, the process can be slow when the maps are large. However, frequently there is a well-founded hypothesis about where particular components are located. In such cases, a local search using a map subvolume will be much faster because the search volume is smaller, and more sensitive because optimizing the search volume for the rotation-search step enhances the signal to noise. A Fourier-space likelihood-based local search approach, based on the previously published em_placement software, has been implemented in the new emplace_local program. Tests confirm that the local search approach enhances the speed and sensitivity of the computations. An interactive graphical interface in the ChimeraX molecular-graphics program provides a convenient way to set up and evaluate docking calculations, particularly in defining the part of the map into which the components should be placed.
59 BASIC BIOLOGICAL SCIENCES↗
Applications of visualization technology in the structural sciences
The structural sciences are undergoing a transformation driven by advancements in visualization technologies that aid researchers in understanding and communicating experimental data from complex molecular systems. New applications of integrative structural biological and biophysical approaches add a wide variety of complementary information from a broad range of scientific disciplines. These approaches extend structural biophysical methodologies to enable research by the incorporation of a variety of data streams and utilization of tools like molecular graphics, virtual reality, and machine learning. To redefine how structural data—particularly from cryo-electron microscopy and x-ray crystallography—are fed forward for scientific exploration and communication, the advances in tools for data visualization and interpretation have been critical. By bringing molecular systems into an interactive three-dimensional space, these novel technologies enhance research workflows, facilitate structure-based drug design, and create engaging educational experiences. Taken together, these visualization innovations are essential tools for advancing the field by making concepts more accessible and compelling.
Eng, Edward T. [New York Structural Biology Center↗
Conformation-independent structural comparison of macromolecules with ProSMART
The Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed to allow local comparative structural analyses independent of the global conformations and sequence homology of the compared macromolecules. This allows quick and intuitive visualization of the conservation of backbone and side-chain conformations, providing complementary information to existing methods. The identification and exploration of (dis)similarities between macromolecular structures can help to gain biological insight, for instance when visualizing or quantifying the response of a protein to ligand binding. Obtaining a residue alignment between compared structures is often a prerequisite for such comparative analysis. If the conformational change of the protein is dramatic, conventional alignment methods may struggle to provide an intuitive solution for straightforward analysis. To make such analyses more accessible, the Procrustes Structural Matching Alignment and Restraints Tool (ProSMART) has been developed, which achieves a conformation-independent structural alignment, as well as providing such additional functionalities as the generation of restraints for use in the refinement of macromolecular models. Sensible comparison of protein (or DNA/RNA) structures in the presence of conformational changes is achieved by enforcing neither chain nor domain rigidity. The visualization of results is facilitated by popular molecular-graphics software such as CCP4mg and PyMOL, providing intuitive feedback regarding structural conservation and subtle dissimilarities between close homologues that can otherwise be hard to identify. Automatically generated colour schemes corresponding to various residue-based scores are provided, which allow the assessment of the conservation of backbone and side-chain conformations relative to the local coordinate frame. Structural comparison tools such as ProSMART can help to break the complexity that accompanies the constantly growing pool of structural data into a more readily accessible form, potentially offering biological insight or influencing subsequent experiments.
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pnnl/mlprotein
The molecular graphics program, PyMol, was employed to produce all images in the training/validation/testing datasets. A PyMol script identified the clusters of interest from a list of all proteins containing 1) Fe (III) and Fe (II) ion and 2) FeS, respectively. A PyMol script and a Python webscraper were also used to classify [2Fe-2S] cofactors into three classes: standard, Rieske, and other and to identify iron atoms with four cysteine residues. We also used the pyMol script to rotate amino acids for training
Oostrom, Marjolein↗
Implementation of the Molecular Electrostatic Potential over Graphics Processing Units
The molecular electrostatic potential (MEP) generated by quantum chemistry methods and Gaussian functions is evaluated over graphics processing units (GPUs). This implementation is based on full-range Rys polynomials with nodes and weights obtained in each thread of a GPU. For high angular moments, the corresponding integral is solved using a one dimension vertical recurrence relation. Thus, we computed the MEP with minimal approximations. We show that this implementation is stable and very efficient since the time consumed over GPUs is quite small compared with similar implementations over CPUs. The implementation was done by using CUDA-C programming techniques within the Graphics Processing Units for Atoms and Molecules (GPUAM) project, which has been designed to analyze quantum chemistry fields over heterogeneous computational resources. With this new scalar field GPUAM is a useful application for the quantum chemistry community, in particular for people interested in chemical reactivity analysis.
Cruz-Monterrosas, Julio-Cesar↗
TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units
Developed over the past decade, TeraChem is an electronic structure and ab initio molecular dynamics software package designed from the ground up to leverage graphics processing units (GPUs) to perform large-scale ground and excited state quantum chemistry calculations in the gas and the condensed phase. TeraChem’s speed stems from the reformulation of conventional electronic structure theories in terms of a set of individually optimized high-performance electronic structure operations (e.g., Coulomb and exchange matrix builds, one- and two-particle density matrix builds) and rank-reduction techniques (e.g., tensor hypercontraction). Recent efforts have encapsulated these core operations and provided language-agnostic interfaces. Finally, this greatly increases the accessibility and flexibility of TeraChem as a platform to develop new electronic structure methods on GPUs and provides clear optimization targets for emerging parallel computing architectures.
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Ab Initio Interactive Molecular Dynamics on Graphical Processing Units (GPUs)
Explore the source record for details and available documents.
Luehr, Nathan↗
High-Performance Semiempirical Excited-State Molecular Dynamics Powered by Graphics Processing Units
Here, this Letter introduces excited-state molecular dynamics in PYSEQM, a GPU-accelerated semiempirical quantum chemistry engine implemented in PyTorch. The new module enables Born–Oppenheimer molecular dynamics (BOMD) using configuration-interaction singles and random phase approximation for excited states, allowing long trajectories and large statistical ensembles to be simulated efficiently on a single GPU. We also implement an extended Lagrangian excited-state BOMD (XL-ESMD) scheme that propagates auxiliary electronic variables, enabling relaxed ground and excited-state convergence thresholds without compromising energy conservation. The excited-state BOMD implementation scales smoothly from small chromophores to a nearly 900-atom dendrimer (taking 6.5 s per MD step). PYSEQM also supports batched execution, allowing many geometries or trajectories to be evaluated in a single GPU launch, substantially increasing throughput and making ensemble-based protocols routine. As a demonstration, we compute absorption, emission, and infrared spectra from trajectories propagated on the ground and first excited states. The XL-ESMD scheme yields identical spectra at significantly lower computational cost, establishing the role of extended Lagrangian based dynamics for efficient excited-state BOMD simulations. Beyond raw performance, PYSEQM’s PyTorch foundation provides automatic differentiation for forces, efficient GPU batching, and seamless interfacing with machine learning models. These capabilities position PYSEQM as a practical platform for machine learning-augmented excited-state dynamics and lay the foundation for future data-driven nonadiabatic excited-state dynamics modeling of ultrafast spectroscopic probes.
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Graphic contrastive learning analyses of discontinuous molecular dynamics simulations: Study of protein folding upon adsorption
A comprehensive understanding of the interfacial behaviors of biomolecules holds great significance in the development of biomaterials and biosensing technologies. In this work, we used discontinuous molecular dynamics (DMD) simulations and graphic contrastive learning analysis to study the adsorption of ubiquitin protein on a graphene surface. Our high-throughput DMD simulations can explore the whole protein adsorption process including the protein structural evolution with sufficient accuracy. Contrastive learning was employed to train a protein contact map feature extractor aiming at generating contact map feature vectors. Subsequently, these features were grouped using the k-means clustering algorithm to identify the protein structural transition stages throughout the adsorption process. The machine learning analysis can illustrate the dynamics of protein structural changes, including the pathway and the rate-limiting step. Our study indicated that the protein–graphene surface hydrophobic interactions and the π–π stacking were crucial to the seven-stage adsorption process. Upon adsorption, the secondary structure and tertiary structure of ubiquitin disintegrated. The unfolding stages obtained by contrastive learning-based algorithm were not only consistent with the detailed analyses of protein structures but also provided more hidden information about the transition states and pathway of protein adsorption process and structural dynamics. Our combination of efficient DMD simulations and machine learning analysis could be a valuable approach to studying the interfacial behaviors of biomolecules.
97 MATHEMATICS AND COMPUTING↗
Observation of divergent La{sup 3+} ion dilute effect in two series of 3-D fluorescent lanthanide-MOFs-based molecular alloys RE{sub x}La{sub 1−x}–EBTC (RE{sup 3+}=Eu{sup 3+} or Tb{sup 3+}; EBTC{sup 4−}=1,1′-ethynebenzene-3,3′,5,5′-etracarboxylate)
The lanthanide metal-organic frameworks (MOFs) [Ln{sub 2}(EBTC){sub 1.5}(CH{sub 3}OH){sub 4}]·6H{sub 2}O are isostructural to each other, where EBTC{sup 4−}=1,1′-ethynebenzene-3,3′,5,5′-tetracarboxylate; Ln{sup 3+}=La{sup 3+}, Eu{sup 3+} and Tb{sup 3+}; and the corresponding MOF is abbreviated as Ln–EBTC. MOFs Eu–EBTC and Tb–EBTC emit intense red and green luminescence (visible by bare eyes), respectively. The molecular alloys of Eu{sub x}La{sub 1−x}–EBTC and Tb{sub x}La{sub 1−x}–EBTC have been successfully prepared by mixing Eu{sup 3+}/Tb{sup 3+} and La{sup 3+} salts with the desired molar ratio in the starting material. Two series of Eu{sub x}La{sub 1−x}–EBTC and Tb{sub x}La{sub 1−x}–EBTC molecular alloys are isomorphic to the parent Ln–EBTC MOFs, while exhibit divergent La{sup 3+} ion diluting effect, namely, with increasing the relative amount of La{sup 3+}, the intensity of characteristic emission arising from Tb{sup 3+} ion monotonely increases in Tb{sub x}La{sub 1−x}–EBTC molecular alloys, whereas that of Eu{sup 3+} ion shows non-monotone decrease in Eu{sub x}La{sub 1−x}–EBTC molecular alloys. The possible origin is discussed for such a divergent behavior between Eu{sub x}La{sub 1−x}–EBTC and Tb{sub x}La{sub 1−x}–EBTC molecular alloys. - Graphical abstract: Two series of 3-D fluorescent lanthanide-MOFs-based molecular alloys RE{sub x}La{sub 1−x}–EBTC (RE{sup 3+}=Eu{sup 3+} or Tb{sup 3+}; EBTC{sup 4−}=1,1′-ethynebenzene-3,3′,5,5′-tetracarboxylate) have been successfully prepared by mixing Eu{sup 3+}/Tb{sup 3+} and La{sup 3+} salts with the desired molar ratio in the starting material and showed photoluminescence property with divergent La{sup 3+} ion dilute effect. - Highlights: • 3-D molecular alloys of Eu{sub x}La{sub 1−x}–EBTC and Tb{sub x}La{sub 1−x}–EBTC were prepared. • They are isomorphic to the parent Ln–EBTC MOFs. • They show photoluminescence property with divergent La{sup 3+} ion diluting effect. • The possible origin is discussed for such a divergent behavior.
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Graphics processing units accelerated semiclassical initial value representation molecular dynamics
This paper presents a Graphics Processing Units (GPUs) implementation of the Semiclassical Initial Value Representation (SC-IVR) propagator for vibrational molecular spectroscopy calculations. The time-averaging formulation of the SC-IVR for power spectrum calculations is employed. Details about the GPU implementation of the semiclassical code are provided. Four molecules with an increasing number of atoms are considered and the GPU-calculated vibrational frequencies perfectly match the benchmark values. The computational time scaling of two GPUs (NVIDIA Tesla C2075 and Kepler K20), respectively, versus two CPUs (Intel Core i5 and Intel Xeon E5-2687W) and the critical issues related to the GPU implementation are discussed. The resulting reduction in computational time and power consumption is significant and semiclassical GPU calculations are shown to be environment friendly.
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Rhorix: An interface between quantum chemical topology and the 3D graphics program blender
Not Available
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Redox-active porous coordination polymer based on trinuclear pivalate: Temperature-dependent crystal rearrangement and redox-behavior
Linking of trinuclear pivalate Fe{sub 2}NiO(Piv){sub 6} (Piv=O{sub 2}CC(CH{sub 3}){sub 3}) by 2,6-bis(4-pyridyl)-4-(1-naphthyl)pyridine (L) resulted in formation of 1D-porous coordination polymer Fe{sub 2}NiO(Piv){sub 6}(L)·Solv, which was characterized in two forms: DMSO solvate Fe{sub 2}NiO(Piv){sub 6}(L)(DMSO)·2.5DMSO (1) or water solvate Fe{sub 2}NiO(Piv){sub 6}(L)(H{sub 2}O) (2). X-ray structure of 1 was determined. Crystal lattice of 1 at 160 K contained open channels, filled by captured solvent, while temperature growth to 296 K led to the crystal lattice rearrangement and formation of closed voids. Redox-behavior of 2 was studied by cyclic voltammetry for a solid compound, deposited on glassy-carbon electrode. Redox-activity of L preserved upon incorporation in the coordination polymer. The presence of pores in desolvated sample Fe{sub 2}NiO(Piv){sub 6}(L) was confirmed by the measurements of N{sub 2} and H{sub 2} adsorption at 77 K. Potential barriers of the different molecules diffusion through pores were estimated by the means of molecular mechanics. - Graphical abstract: Redox-behavior of 1D-porous coordination polymer Fe{sub 2}NiO(Piv){sub 6}(L)(H{sub 2}O) was studied by cyclic voltammetry in thin film, deposited on glassy-carbon electrode. Redox-activity of L preserved upon incorporation in the coordination polymer. Potential barriers of different molecules diffusion through pores were estimated by the means of molecular mechanics. - Highlights: • Porous 1D coordination polymer was synthesized. • Temperature growth led to pores closing due to crystal lattice rearrangement. • Redox-activity of ligand preserved upon incorporation into coordination polymer. • Redox-properties of solid coordination polymer were studied in thin film. • Diffusion barriers were evaluated by molecular mechanics.
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Unraveling the multi-functional behavior in a series of Metal Organic Frameworks
Three new 2D/3D Metal-Organic Frameworks (MOFs), ([Zn(2,6-ndc)(aldrithiol)]·3(H{sub 2}O)){sub n} (1), ([Co(2,6-ndc)(aldrithiol)(H{sub 2}O){sub 2}]·2(H{sub 2}O)){sub n} (2), ([Cd{sub 2}(2,6-ndc){sub 2}(aldrithiol){sub 2}(H{sub 2}O){sub 2}]·(aldrithiol)·(EtOH)·3(H{sub 2}O)){sub n} (3), (2,6-ndc = 2,6-naphthalene dicarboxylic acid; aldrithiol = 4,4'-dipyridyl disulphide) have been synthesized and structurally characterized. Compounds 1 and 2 have 2D layered architectures with similar framework topology whereas 3 is a 2-fold interwoven three dimensional framework. Sorption studies reveal that compounds 1-3 selectively adsorbs CO{sub 2} over other gases and H{sub 2}O over other solvents. Proton conductivity study of compounds 1 and 2 show highest values of 6.73 x 10{sup -7} S.cm{sup -1}, 1.96 x 10{sup -5} S.cm{sup -1} at 318 K and 95% RH and these values are humidity dependent. Photoluminescent properties of compounds 1 and 3 show metal perturbed (π*–π and π*-n) intra ligand charge transfer transitions. Additionally, Compound 3 also displays reversible adsorption of molecular iodine. - Graphical abstarct: Three new 2D/3D interpenetrated MOFs are synthesized and their multifunctional material properties such as adsorption, proton conduction, iodine adsorption as well as luminscence have been explored. - Highlights: • We report multifunctional material properties in a series MOFs (Compounds 1-3) • All the compounds show selective adsorption of CO{sub 2} over other gases and H{sub 2}O over other solvents. • The proton conduction property studies of all the compounds reveal the humidity dependent conductivity. • Compound 2 shows reversible adsorption of molecular iodine in the framework. • Photoluminescent properties of compounds 1 and 2 show metal perturbed intra ligand charge transfer transitions.
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RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D
We report the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the US National Science Foundation, National Institutes of Health, and Department of Energy, has served structural biologists and Protein Data Bank (PDB) data consumers worldwide since 1999. RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, is the US data center for the global PDB archive housing biomolecular structure data. RCSB PDB is also responsible for the security of PDB data, as the wwPDB-designated Archive Keeper. Annually, RCSB PDB serves tens of thousands of three-dimensional (3D) macromolecular structure data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) from all inhabited continents. RCSB PDB makes PDB data available from its research-focused RCSB.org web portal at no charge and without usage restrictions to millions of PDB data consumers working in every nation and territory worldwide. In addition, RCSB PDB operates an outreach and education PDB101.RCSB.org web portal that was used by more than 800,000 educators, students, and members of the public during calendar year 2020. This invited Tools Issue contribution describes (i) how the archive is growing and evolving as new experimental methods generate ever larger and more complex biomolecular structures; (ii) the importance of data standards and data remediation in effective management of the archive and facile integration with more than 50 external data resources; and (iii) new tools and features for 3D structure analysis and visualization made available during the past year via the RCSB.org web portal.
59 BASIC BIOLOGICAL SCIENCES↗
Synthesis, crystal structure and optical property of three coordination polymer constructed from m-phenylenediacrylate acid
Three new complexes of the wholly deprotonated flexible ligand m-phenylenediacrylate acid (H{sub 2}mpda), namely, [Zn (mpda) (H{sub 2}O)] [1], [Pr{sub 2}(mpda){sub 2}(H{sub 2}O){sub 2}(CHOO){sub 2}] [2], and [Mn{sub 2}(mpda){sub 2} (H{sub 2}O){sub 4}] [3], were synthesized by the solvothermal reaction. The complexes were characterized by IR spectroscopy, thermogravimetric analysis, and X-ray single-crystal diffraction. A mixed sample [Nd(mpda)(H{sub 2}O)(CHOO)·Pr(mpda)(H{sub 2}O)(CHOO)] [2{sup ]} was also synthesized and studied. Compounds [1] and [2] exhibit a selective sensing function with respect to acetone, and they are a potential luminescent sensory material for the selective detection of Zn{sup 2+} and Ni{sup 2+} ions, respectively. Furthermore, the fluorescent changes of compound [1] upon the addition of cations (Fe{sup 3+} and Zn{sup 2+}, Bi{sup 2+} and Zn{sup 2+}) are utilized to construct two logic gates at the molecular level. - Graphical abstract: Three new complexes of flexible ligand m-phenylenedicarboxylic acid were synthesized by solvothermal reaction. Three metal−organic frameworks exhibiting 1D, 2D, 3D structures, respectively. - Highlights: • Three new complexes of m-phenylenedicarboxylic acid were synthesized. • Three metal−organic frameworks exhibiting 1D, 2D, 3D structures, respectively. • [1] and [2] exhibits a very high quenching effect with acetone. • [1] and [2] are a potential luminescent sensory material for Zn{sup 2+}, Ni{sup 2+} ions. • Two logic gates have been constructed using compound [1].
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Spectral, mechanical, thermal, optical and solid state parameters, of metal-organic bis(hydrogenmaleate)-CO(II) tetrahydrate crystal
Metal-organic bis(hydrogenmaleate)-Co(II) tetrahydrate single crystals have been grown by slow evaporation solution growth technique at room temperature. The crystal structure and the unit cell parameters were analyzed from the X-ray diffraction studies. Single-crystal X-ray diffraction analyses reveal that the grown crystal belongs to triclinic system with the space group P-1. Functional groups in bis(hydrogenmaleate)-Co(II) tetrahydrate were identified by Fourier transform infrared spectral analysis. The peak observed at 663 cm{sup −1} is assigned to the (Co–O) stretching vibrations. The optical transmission of the crystal was studied by UV–vis–NIR spectral analysis. The photoluminescence emission studies were carried out for the title compound in a wide wavelength range between 350 nm and 550 nm at 303 K. Mechanical strength was tested by Vickers microhardness test. The laser damage threshold value has been determined using Nd:YAG laser operating at 1064 nm. At various frequencies and temperatures the dielectric behavior of the material was investigated. Solid state parameters such as plasma energy, Penn gap, Fermi energy and electronic polarizability were evaluated. Photoconductivity measurements were carried out for the grown crystal in the presence of DC electric field at room temperature. Thermal stability and decomposition of the crystal were studied by TG–DTA. The weight loss of the title compound occurs in different steps. - Graphical abstract: Molecular structure of the bis(hydrogenmaleate)-Co(II) tetrahydrate drawn at 40% ellipsoid probability level. - Highlights: • Bis(hydrogenmaleate)-Co(II) tetrahydrate single crystal is grown by slow evaporation method. • Structural and optical properties were discussed. • The title complex crystal is thermally stable up to 91 °C. • Plasma energy, Fermi energy and electronic polarizability are evaluated. • It exhibits positive photoconductivity.
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