Journal: Journal of chemical information and modeling

Article Title: BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping

doi: 10.1021/acs.jcim.9b00020

Figure Lengend Snippet: RMSD to native binding pose as a function of maximum common substructure similarity across the AstraZeneca overlay sets. Comparisons were made for all molecule pairs (A), the best alignment for each molecule as measured by symmetry RMSD to the native pose (B), and for all pairs with a symmetry RMSD to native pose ≤2.0 Å (C). The substructures were defined by comparing the atom by element IDs and the bonds by bond order (including specification of aromaticity and/or inclusion in a ring). Similarity between each molecule pair is the maximum common substructure Tanimoto similarity.

Article Snippet: These results suggest that higher 2D similarity can increase the likelihood of recovering the native binding pose but that BCL::MolAlign recovers a large fraction of native binding poses by aligning dissimilar molecules. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 4. caption a7 RMSD to native binding pose as a function of maximum common substructure similarity across the AstraZeneca overlay sets.

Techniques: Binding Assay

Journal: Journal of chemical information and modeling

Article Title: BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping

doi: 10.1021/acs.jcim.9b00020

Figure Lengend Snippet: Comparison between BCL::MolAlign and Maximum Common Substructure-Based Alignment of Congeneric Ligands

Article Snippet: These results suggest that higher 2D similarity can increase the likelihood of recovering the native binding pose but that BCL::MolAlign recovers a large fraction of native binding poses by aligning dissimilar molecules. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window Figure 4. caption a7 RMSD to native binding pose as a function of maximum common substructure similarity across the AstraZeneca overlay sets.

Techniques: Comparison

Journal: The Journal of Physical Chemistry. B

Article Title: Structural Intermediates in a Model of the Substrate Translocation Path of the Bacterial Glutamate Transporter Homologue GltPh

doi: 10.1021/jp301726s

Figure Lengend Snippet: RMSD landscape of all computed conformations along the modeled translocation path of GltPh. Monomer C α -RMSDs with respect to the A monomer in the OfCC crystal structure (RMSD OfCC.A ) are plotted against the ones calculated with respect to monomer A of the IfCC crystal structure (RMSD IfCC.A ) for all modeled MP monomers (“MP O2I ” and “MP I2O ”, black and gray filled circles, respectively); values of representative PRi. x ( x = 2, 4, 5, 11, 12) intermediates are included. All monomers of the starting MDi. x ( x = 2, 4, 5, 11, 12) intermediates and crystal monomer conformations are included (color-filled diamonds: OfCC in yellow, PRi.2/starting MDi.2 in magenta, PRi.4/starting MDi.4 in cyan, PRi.5/starting MDi.5 in white, PRi.11/starting MDi.11, orange, PRi.12/starting MDi.12, purple, and IfCC, brown). Red, blue, and green arrows point to the values for the corresponding monomers (monomers A, B, and C, respectively) after the MD simulations done in the context of the trimer. The linear interpolation between the two crystal structures is drawn as a black dashed line.

Article Snippet: This observation is recorded by smaller values of RMSD OfCC.A (and larger RMSD IfCC.A ) for monomers B and C than for monomer A (Figure ).

Techniques: Translocation Assay

Journal: Journal of Biomolecular Structure & Dynamics

Article Title: Virtual screening of approved clinic drugs with main protease (3CL pro ) reveals potential inhibitory effects on SARS-CoV-2

doi: 10.1080/07391102.2020.1817786

Figure Lengend Snippet: Analysis of molecular dynamics simulation results of the free 3CL pro and the 3CL pro –drug complex. (A) Root mean square deviation (RMSD) of the 3CL pro –Viomycin complex and the free 3CL pro . (B) Intermolecular hydrogen bonds between the Viomycin and the 3CL pro . (C) RMSD of the 3CL pro –Carfilzomib complex and the free 3CL pro . (D) Intermolecular hydrogen bonds between the Carfilzomib and 3CL pro . (E) RMSD of the 3CL pro –Capastat complex and the free 3CL pro . (F) Intermolecular hydrogen bonds between the Capastat and 3CL pro . (G) RMSD of the 3CL pro –Saquinavir complex and the free 3CL pro . (H) Intermolecular hydrogen bonds between the Saquinavir and 3CL pro .

Article Snippet: The graphs of RMSD and hydrogen bonds were plotted using GraphPad.

Techniques:

Journal: Journal of Biomolecular Structure & Dynamics

Article Title: Virtual screening of approved clinic drugs with main protease (3CL pro ) reveals potential inhibitory effects on SARS-CoV-2

doi: 10.1080/07391102.2020.1817786

Figure Lengend Snippet: Analysis of molecular dynamics simulation results of the free 3CL pro and the 3CL pro –drug complex. (A) RMSD of the 3CL pro –Lopinavir complex and the free 3CL pro . (B) Intermolecular hydrogen bonds between the Lopinavir and 3CL pro .

Article Snippet: The graphs of RMSD and hydrogen bonds were plotted using GraphPad.

Techniques:

Journal: Journal of Chemical Information and Modeling

Article Title: Best of Both Worlds: On the Complementarity of Ligand-Based and Structure-Based Virtual Screening

doi: 10.1021/ci5001604

Figure Lengend Snippet: Docking success rate for three Glide protocols: HTVS, SP, and XP. Docking pose prediction is considered correct if the RMSD from the crystallographic ligand is below 2 Å.

Article Snippet: The RMSD of the heavy atoms of the docked ligand from the prealigned crystallographic ligand was calculated using the KNIME node RMSD (MOE).

Techniques: