cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.11532999
title: Structure-based virtual screening, free energy of binding and molecular dynamics simulations to propose novel inhibitors of Mtb-MurB oxidoreductase enzyme

description: Currently, the growing incidence of drug resistance toward tuberculosis intensified the need for discovery of novel targets and their inhibitors. The enzyme MurB which is involved in one of the steps for peptidoglycan biosynthesis is an effective target that can produce drugs having lesser side-effects. Recently the only crystal structure of Mycobacterium Tuberculosis MurB has been deposited and, therefore, in the present study, we have used this as a target for virtual screening of drug-like molecules from the ZINC Database. We have also designed a complete workflow for the process which resulted in 12 hit compounds that have good docking scores, Δ<i>G<sub>bind</sub></i>, and Glide energy. The hits obtained have also been found to share structural features with some known antibiotics such as Amoxicillin. Furthermore, MD simulations on the top most hit L1 displayed its stable binding with the enzyme. Thus, this study has proved helpful in proposing novel inhibitors for MurB enzyme that can be tested against various TB strains. Communicated by Ramaswamy H. Sarma
DOI: 10.17188/1689228
title: Materials Data on MgGaPt2 by Materials Project

description: MgPt2Ga crystallizes in the orthorhombic Immm space group. The structure is one-dimensional and consists of two MgPt2Ga ribbons oriented in the (1, 0, 0) direction. Mg2+ is bonded in a linear geometry to two equivalent Pt2- atoms. Both Mg–Pt bond lengths are 2.48 Å. Pt2- is bonded in a linear geometry to one Mg2+ and one Ga2+ atom. The Pt–Ga bond length is 2.31 Å. Ga2+ is bonded in a linear geometry to two equivalent Pt2- atoms.
DOI: 10.17188/1689229
title: Materials Data on Dy(SiPt)2 by Materials Project

description: Dy(PtSi)2 crystallizes in the tetragonal I4/mmm space group. The structure is three-dimensional. Dy is bonded in a 8-coordinate geometry to eight equivalent Pt and eight equivalent Si atoms. All Dy–Pt bond lengths are 3.27 Å. All Dy–Si bond lengths are 3.28 Å. Pt is bonded in a 4-coordinate geometry to four equivalent Dy and four equivalent Si atoms. All Pt–Si bond lengths are 2.41 Å. Si is bonded in a 4-coordinate geometry to four equivalent Dy and four equivalent Pt atoms.
DOI: 10.17188/1689230
title: Materials Data on Dy2Re3Si5 by Materials Project

description: Dy2Re3Si5 crystallizes in the tetragonal P4/mnc space group. The structure is three-dimensional. Dy3+ is bonded in a 9-coordinate geometry to nine Si4- atoms. There are a spread of Dy–Si bond distances ranging from 2.85–3.23 Å. There are two inequivalent Re+4.67+ sites. In the first Re+4.67+ site, Re+4.67+ is bonded to six Si4- atoms to form a mixture of distorted corner, edge, and face-sharing ReSi6 octahedra. The corner-sharing octahedral tilt angles are 49°. There are a spread of Re–Si bond distances ranging from 2.48–2.55 Å. In the second Re+4.67+ site, Re+4.67+ is bonded in a distorted hexagonal planar geometry to six Si4- atoms. There are four shorter (2.48 Å) and two longer (2.69 Å) Re–Si bond lengths. There are three inequivalent Si4- sites. In the first Si4- site, Si4- is bonded in a 9-coordinate geometry to three equivalent Dy3+, four Re+4.67+, and two equivalent Si4- atoms. Both Si–Si bond lengths are 2.61 Å. In the second Si4- site, Si4- is bonded in a 11-coordinate geometry to four equivalent Dy3+, three Re+4.67+, and four Si4- atoms. Both Si–Si bond lengths are 2.78 Å. In the third Si4- site, Si4- is bonded in a 9-coordinate geometry to four equivalent Dy3+, four equivalent Re+4.67+, and one Si4- atom. The Si–Si bond length is 2.71 Å.
DOI: 10.17188/1689231
title: Materials Data on Nb2MoRu by Materials Project

description: Nb2MoRu is Heusler structured and crystallizes in the cubic Fm-3m space group. The structure is three-dimensional. Nb is bonded in a body-centered cubic geometry to four equivalent Mo and four equivalent Ru atoms. All Nb–Mo bond lengths are 2.78 Å. All Nb–Ru bond lengths are 2.78 Å. Mo is bonded in a body-centered cubic geometry to eight equivalent Nb atoms. Ru is bonded in a body-centered cubic geometry to eight equivalent Nb atoms.
DOI: 10.6084/m9.figshare.11506587
title: Identifying the key residues instrumental in imparting stability to amyloid beta protofibrils – a comparative study using MD simulations of 17–42 residues

description: Extracellular plaques, the hallmark of Alzheimer’s disease brains, consist of insoluble amyloid fibrils that result from the aggregation of amyloid beta peptides. None of the few therapeutic options currently adopted, address the cause of the disease. Instead, they reduce symptom of the disease. Inhibition of aggregation or destabilization of aggregates therefore, emerges as a preferable therapeutic approach. Designing inhibitors or destabilizers demands comprehensive knowledge of the residues of amyloid beta responsible for the phenomenal structural stability of the aggregate. For the purpose, we have compared the effect on structural destabilization of 13 <i>in silico</i> mutations (single and double) with the wild type counterpart of beta-strand-turn-beta-strand motif of the amyloid beta protofibrils by molecular dynamics simulation. Besides the already known salt bridge interaction between K28 and D23, our analyses expose more significant role of K28 as the only positive charge present in the vicinity. Amongst the two consecutive aromatic residues, F19 is involved in stacking interaction; although effect of F20 mutation is more pronounced. Face to face arrangement of A21 and V36 acts as a pillar maintaining the necessary optimum distance between consecutive chains to promote stabilizing interactions. In addition to providing stability to the first beta-strand, large sized negatively charged E22 facilitates salt bridge formation by ensuring fixed relative position of D23 and in turn K28. Likewise, the hydrophobic residues I32 and L34 pack the protofibril core, once again fostering salt bridge interaction. Prospectively, these findings may be compiled for efficient identification or design of scaffolds accountable for protofibril destabilization. Communicated by Ramaswamy H. Sarma
DOI: 10.17188/1689232
title: Materials Data on CsNiBr3 by Materials Project

description: CsNiBr3 crystallizes in the hexagonal P6_3/mmc space group. The structure is three-dimensional. Cs1+ is bonded to twelve equivalent Br1- atoms to form CsBr12 cuboctahedra that share corners with six equivalent CsBr12 cuboctahedra, corners with six equivalent NiBr6 octahedra, faces with eight equivalent CsBr12 cuboctahedra, and faces with six equivalent NiBr6 octahedra. The corner-sharing octahedral tilt angles are 15°. There are six shorter (3.85 Å) and six longer (3.98 Å) Cs–Br bond lengths. Ni2+ is bonded to six equivalent Br1- atoms to form NiBr6 octahedra that share corners with six equivalent CsBr12 cuboctahedra, faces with six equivalent CsBr12 cuboctahedra, and faces with two equivalent NiBr6 octahedra. All Ni–Br bond lengths are 2.57 Å. Br1- is bonded in a 6-coordinate geometry to four equivalent Cs1+ and two equivalent Ni2+ atoms.
DOI: 10.17188/1689233
title: Materials Data on Li3MnF6 by Materials Project

description: Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations
DOI: 10.17188/1689235
title: Materials Data on Sr2LuUO6 by Materials Project

description: Sr2ULuO6 is (Cubic) Perovskite-derived structured and crystallizes in the cubic Fm-3m space group. The structure is three-dimensional. Sr2+ is bonded to twelve equivalent O2- atoms to form SrO12 cuboctahedra that share corners with twelve equivalent SrO12 cuboctahedra, faces with six equivalent SrO12 cuboctahedra, faces with four equivalent UO6 octahedra, and faces with four equivalent LuO6 octahedra. All Sr–O bond lengths are 3.04 Å. U5+ is bonded to six equivalent O2- atoms to form UO6 octahedra that share corners with six equivalent LuO6 octahedra and faces with eight equivalent SrO12 cuboctahedra. The corner-sharing octahedral tilt angles are 0°. All U–O bond lengths are 2.14 Å. Lu3+ is bonded to six equivalent O2- atoms to form LuO6 octahedra that share corners with six equivalent UO6 octahedra and faces with eight equivalent SrO12 cuboctahedra. The corner-sharing octahedral tilt angles are 0°. All Lu–O bond lengths are 2.17 Å. O2- is bonded in a distorted linear geometry to four equivalent Sr2+, one U5+, and one Lu3+ atom.
DOI: 10.17188/1689236
title: Materials Data on V11NiO18 by Materials Project

description: Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations
DOI: 10.17188/1689237
title: Materials Data on Si11(H3C)21 by Materials Project

description: Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations
DOI: 10.17188/1689238
title: Materials Data on TiCu2Au by Materials Project

description: TiAuCu2 crystallizes in the orthorhombic Immm space group. The structure is one-dimensional and consists of two TiAuCu2 ribbons oriented in the (0, 1, 0) direction. Ti is bonded in a linear geometry to two equivalent Cu atoms. Both Ti–Cu bond lengths are 2.39 Å. Au is bonded in a linear geometry to two equivalent Cu atoms. Both Au–Cu bond lengths are 2.44 Å. Cu is bonded in a linear geometry to one Ti and one Au atom.
DOI: 10.17188/1689239
title: Materials Data on Cd2SnO4 by Materials Project

description: Cd2SnO4 is Spinel structured and crystallizes in the cubic Fd-3m space group. The structure is three-dimensional. Cd2+ is bonded to six equivalent O2- atoms to form CdO6 octahedra that share corners with six equivalent SnO4 tetrahedra and edges with six equivalent CdO6 octahedra. All Cd–O bond lengths are 2.34 Å. Sn4+ is bonded to four equivalent O2- atoms to form SnO4 tetrahedra that share corners with twelve equivalent CdO6 octahedra. The corner-sharing octahedral tilt angles are 54°. All Sn–O bond lengths are 2.01 Å. O2- is bonded in a rectangular see-saw-like geometry to three equivalent Cd2+ and one Sn4+ atom.
DOI: 10.17188/1689240
title: Materials Data on YN3O14 by Materials Project

description: Y(NO4)3O2 crystallizes in the triclinic P-1 space group. The structure is zero-dimensional and consists of two oxygen molecules and two Y(NO4)3 clusters. In each Y(NO4)3 cluster, Y is bonded in a distorted hexagonal bipyramidal geometry to eight O atoms. There are a spread of Y–O bond distances ranging from 2.25–2.71 Å. There are three inequivalent N sites. In the first N site, N is bonded in a trigonal planar geometry to three O atoms. There are a spread of N–O bond distances ranging from 1.22–1.30 Å. In the second N site, N is bonded in a trigonal planar geometry to three O atoms. There are a spread of N–O bond distances ranging from 1.22–1.31 Å. In the third N site, N is bonded in a trigonal planar geometry to three O atoms. There are a spread of N–O bond distances ranging from 1.21–1.31 Å. There are twelve inequivalent O sites. In the first O site, O is bonded in a water-like geometry to one Y and one O atom. The O–O bond length is 1.24 Å. In the second O site, O is bonded in a distorted L-shaped geometry to one Y and one N atom. In the third O site, O is bonded in a distorted L-shaped geometry to one Y and one N atom. In the fourth O site, O is bonded in a single-bond geometry to one N atom. In the fifth O site, O is bonded in a distorted water-like geometry to one Y and one N atom. In the sixth O site, O is bonded in a distorted L-shaped geometry to one Y and one N atom. In the seventh O site, O is bonded in a single-bond geometry to one N atom. In the eighth O site, O is bonded in an L-shaped geometry to one Y and one N atom. In the ninth O site, O is bonded in an L-shaped geometry to one Y and one N atom. In the tenth O site, O is bonded in a single-bond geometry to one N atom. In the eleventh O site, O is bonded in a single-bond geometry to one Y atom. In the twelfth O site, O is bonded in a single-bond geometry to one O atom.
DOI: 10.17188/1689241
title: Materials Data on LiVP4O13 by Materials Project

description: Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations
DOI: 10.17188/1689243
title: Materials Data on Rb8BiO3 by Materials Project

description: Rb8BiO3 crystallizes in the cubic Pm-3m space group. The structure is three-dimensional. Rb is bonded to one Bi and three equivalent O atoms to form a mixture of distorted edge and corner-sharing RbBiO3 tetrahedra. The Rb–Bi bond length is 3.49 Å. All Rb–O bond lengths are 3.16 Å. Bi is bonded in a body-centered cubic geometry to eight equivalent Rb atoms. O is bonded in a body-centered cubic geometry to eight equivalent Rb atoms.
DOI: 10.17188/1689244
title: Materials Data on V3OF7 by Materials Project

description: Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations
DOI: 10.17188/1689245
title: Materials Data on Na3YI6 by Materials Project

description: Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations
DOI: 10.17188/1689246
title: Materials Data on Li13Mn8O24 by Materials Project

description: Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations
DOI: 10.17188/1689247
title: Materials Data on La2CdIn by Materials Project

description: La2CdIn crystallizes in the orthorhombic Immm space group. The structure is one-dimensional and consists of two La2CdIn ribbons oriented in the (1, 0, 0) direction. La is bonded in a linear geometry to one Cd and one In atom. The La–Cd bond length is 3.14 Å. The La–In bond length is 2.98 Å. Cd is bonded in a linear geometry to two equivalent La atoms. In is bonded in a linear geometry to two equivalent La atoms.
DOI: 10.17188/1689248
title: Materials Data on LiMnPCO7 by Materials Project

description: Computed materials data using density functional theory calculations. These calculations determine the electronic structure of bulk materials by solving approximations to the Schrodinger equation. For more information, see https://materialsproject.org/docs/calculations
DOI: 10.17188/1689249
title: Materials Data on Tb(SiIr)2 by Materials Project

description: TbIr2Si2 crystallizes in the tetragonal P4/nmm space group. The structure is three-dimensional. Tb is bonded in a 8-coordinate geometry to eight Ir and eight Si atoms. There are four shorter (3.15 Å) and four longer (3.26 Å) Tb–Ir bond lengths. There are four shorter (3.17 Å) and four longer (3.19 Å) Tb–Si bond lengths. There are two inequivalent Ir sites. In the first Ir site, Ir is bonded to four equivalent Tb and four equivalent Si atoms to form distorted IrTb4Si4 tetrahedra that share corners with twelve equivalent SiTb4Ir4 tetrahedra, edges with two equivalent SiTb4Ir4 tetrahedra, edges with four equivalent IrTb4Si4 tetrahedra, and faces with four equivalent IrTb4Si4 tetrahedra. All Ir–Si bond lengths are 2.44 Å. In the second Ir site, Ir is bonded in a 9-coordinate geometry to four equivalent Tb and five Si atoms. There are one shorter (2.38 Å) and four longer (2.43 Å) Ir–Si bond lengths. There are two inequivalent Si sites. In the first Si site, Si is bonded to four equivalent Tb and four equivalent Ir atoms to form distorted SiTb4Ir4 tetrahedra that share corners with twelve equivalent IrTb4Si4 tetrahedra, edges with two equivalent IrTb4Si4 tetrahedra, edges with four equivalent SiTb4Ir4 tetrahedra, and faces with four equivalent SiTb4Ir4 tetrahedra. In the second Si site, Si is bonded in a 9-coordinate geometry to four equivalent Tb and five Ir atoms.
DOI: 10.17188/1689250
title: Materials Data on Zr2PdPt by Materials Project

description: Zr2PtPd crystallizes in the orthorhombic Immm space group. The structure is one-dimensional and consists of two Zr2PtPd ribbons oriented in the (1, 0, 0) direction. Zr is bonded in a linear geometry to one Pt and one Pd atom. The Zr–Pt bond length is 2.47 Å. The Zr–Pd bond length is 2.54 Å. Pt is bonded in a linear geometry to two equivalent Zr atoms. Pd is bonded in a linear geometry to two equivalent Zr atoms.
DOI: 10.17188/1689253
title: Materials Data on K2LiNbF6 by Materials Project

description: K2LiNbF6 is (Cubic) Perovskite-derived structured and crystallizes in the cubic Fm-3m space group. The structure is three-dimensional. K1+ is bonded to twelve equivalent F1- atoms to form KF12 cuboctahedra that share corners with twelve equivalent KF12 cuboctahedra, faces with six equivalent KF12 cuboctahedra, faces with four equivalent LiF6 octahedra, and faces with four equivalent NbF6 octahedra. All K–F bond lengths are 2.96 Å. Li1+ is bonded to six equivalent F1- atoms to form LiF6 octahedra that share corners with six equivalent NbF6 octahedra and faces with eight equivalent KF12 cuboctahedra. The corner-sharing octahedral tilt angles are 0°. All Li–F bond lengths are 2.08 Å. Nb3+ is bonded to six equivalent F1- atoms to form NbF6 octahedra that share corners with six equivalent LiF6 octahedra and faces with eight equivalent KF12 cuboctahedra. The corner-sharing octahedral tilt angles are 0°. All Nb–F bond lengths are 2.11 Å. F1- is bonded in a distorted linear geometry to four equivalent K1+, one Li1+, and one Nb3+ atom.
DOI: 10.17188/1689254
title: Materials Data on Na2AsO8 by Materials Project

description: Na2AsO8 crystallizes in the orthorhombic P2_12_12 space group. The structure is three-dimensional. there are two inequivalent Na sites. In the first Na site, Na is bonded in a 5-coordinate geometry to six O atoms. There are a spread of Na–O bond distances ranging from 2.39–2.99 Å. In the second Na site, Na is bonded in a 7-coordinate geometry to seven O atoms. There are a spread of Na–O bond distances ranging from 2.39–2.66 Å. As is bonded in a trigonal planar geometry to three O atoms. All As–O bond lengths are 1.67 Å. There are nine inequivalent O sites. In the first O site, O is bonded in a trigonal planar geometry to three Na atoms. In the second O site, O is bonded in a 3-coordinate geometry to two Na and one O atom. The O–O bond length is 1.24 Å. In the third O site, O is bonded in a distorted rectangular see-saw-like geometry to two equivalent Na and two equivalent O atoms. Both O–O bond lengths are 1.33 Å. In the fourth O site, O is bonded in a linear geometry to two equivalent Na atoms. In the fifth O site, O is bonded in a bent 150 degrees geometry to one Na and one As atom. In the sixth O site, O is bonded in a single-bond geometry to one O atom. In the seventh O site, O is bonded in a distorted bent 150 degrees geometry to one Na and one As atom. In the eighth O site, O is bonded in a 3-coordinate geometry to two equivalent Na and one O atom. In the ninth O site, O is bonded in a trigonal planar geometry to two equivalent Na and one As atom.
DOI: 10.17188/1689255
title: Materials Data on NbMo by Materials Project

description: NbMo crystallizes in the orthorhombic Cmmm space group. The structure is two-dimensional and consists of two NbMo sheets oriented in the (0, 1, 0) direction. Nb is bonded in a 4-coordinate geometry to four equivalent Mo atoms. All Nb–Mo bond lengths are 2.79 Å. Mo is bonded in a 4-coordinate geometry to four equivalent Nb atoms.
DOI: 10.17188/1689256
title: Materials Data on NiH12(C2O5)2 by Materials Project

description: Ni(HO)4(C2O)2(H2O)4 crystallizes in the monoclinic P2_1/c space group. The structure is zero-dimensional and consists of two 1,3-butadiyne-1,4-diol molecules; eight water molecules; and two Ni(HO)4 clusters. In each Ni(HO)4 cluster, Ni2+ is bonded in a square co-planar geometry to four O2- atoms. There is two shorter (1.69 Å) and two longer (1.95 Å) Ni–O bond length. There are two inequivalent H1+ sites. In the first H1+ site, H1+ is bonded in a single-bond geometry to one O2- atom. The H–O bond length is 0.98 Å. In the second H1+ site, H1+ is bonded in a single-bond geometry to one O2- atom. The H–O bond length is 0.99 Å. There are two inequivalent O2- sites. In the first O2- site, O2- is bonded in a single-bond geometry to one Ni2+ atom. In the second O2- site, O2- is bonded in a distorted water-like geometry to one Ni2+ and two H1+ atoms.
DOI: 10.17188/1689257
title: Materials Data on Zn2P2O11F2 by Materials Project

description: Zn2P2O11F2 crystallizes in the triclinic P-1 space group. The structure is three-dimensional. there are three inequivalent Zn sites. In the first Zn site, Zn is bonded in a distorted linear geometry to four O atoms. There are two shorter (1.79 Å) and two longer (2.51 Å) Zn–O bond lengths. In the second Zn site, Zn is bonded in a square co-planar geometry to four O atoms. There are two shorter (1.87 Å) and two longer (2.22 Å) Zn–O bond lengths. In the third Zn site, Zn is bonded to four O atoms to form ZnO4 tetrahedra that share corners with four PO3F tetrahedra. There are a spread of Zn–O bond distances ranging from 1.94–1.98 Å. There are two inequivalent P sites. In the first P site, P is bonded to three O and one F atom to form PO3F tetrahedra that share corners with two equivalent ZnO4 tetrahedra. There is two shorter (1.51 Å) and one longer (1.55 Å) P–O bond length. The P–F bond length is 1.58 Å. In the second P site, P is bonded to three O and one F atom to form PO3F tetrahedra that share corners with two equivalent ZnO4 tetrahedra. There are a spread of P–O bond distances ranging from 1.51–1.55 Å. The P–F bond length is 1.58 Å. There are eleven inequivalent O sites. In the first O site, O is bonded in a distorted bent 120 degrees geometry to one Zn and one P atom. In the second O site, O is bonded in a bent 150 degrees geometry to one Zn and one P atom. In the third O site, O is bonded in a bent 120 degrees geometry to one Zn and one P atom. In the fourth O site, O is bonded in a bent 150 degrees geometry to one Zn and one P atom. In the fifth O site, O is bonded in a distorted bent 120 degrees geometry to one Zn and one P atom. In the sixth O site, O is bonded in a distorted bent 120 degrees geometry to one Zn and one P atom. In the seventh O site, O is bonded in a single-bond geometry to one O atom. The O–O bond length is 1.26 Å. In the eighth O site, O is bonded in a bent 120 degrees geometry to two O atoms. The O–O bond length is 1.33 Å. In the ninth O site, O is bonded in an L-shaped geometry to one Zn and one O atom. The O–O bond length is 1.24 Å. In the tenth O site, O is bonded in a bent 120 degrees geometry to one Zn and one O atom. In the eleventh O site, O is bonded in a single-bond geometry to one O atom. There are two inequivalent F sites. In the first F site, F is bonded in a single-bond geometry to one P atom. In the second F site, F is bonded in a single-bond geometry to one P atom.
DOI: 10.17188/1689259
title: Materials Data on W(Br3N)2 by Materials Project

description: WBr6N2 is Fluorite structured and crystallizes in the cubic Fm-3m space group. The structure is zero-dimensional and consists of eight ammonia molecules and four hexabromotungsten molecules.