fconv: format conversion, manipulation and feature computation of molecular data

Neudert, Gerd; Klebe, G.

doi:10.1093/bioinformatics/btr055

Cited by 68 publications

(68 citation statements)

References 9 publications

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“…As hypothesized, the cyano-pyrimidine warhead of both ligands binds to Cdu1 in a similar way as to adenain with an RMSD [34] over the heavy atoms of the warhead of 0.56 Å for 3 and 1.57 Å for 5 (Figure 4B, right). There are, however, a few key differences in the binding modes beyond the covalent warhead.…”

Section: Resultsmentioning

confidence: 69%

Structural Basis of Substrate Recognition and Covalent Inhibition of Cdu1 from Chlamydia trachomatis

et al. 2018

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Based on the similarity between the active sites of the deubiquitylating and deneddylating enzyme ChlaDub1 (Cdu1) and the evolutionarily related protease adenain, a target-hopping screening approach on a focused set of adenain inhibitors was investigated. The cyanopyrimidine-based inhibitors identified represent the first active-site-directed small-molecule inhibitors of Cdu1. High-resolution crystal structures of Cdu1 in complex with two covalently bound cyanopyrimidines, as well as with its substrate ubiquitin, were obtained. These structural data were complemented by enzymatic assays and covalent docking studies to provide insight into the substrate recognition of Cdu1, active-site pocket flexibility and potential hotspots for ligand interaction. Combined, these data provide a strong basis for future structure-guided medicinal chemistry optimization of this cyanopyrimidine scaffold into more potent and selective Cdu1 inhibitors.

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Section: Resultsmentioning

confidence: 69%

Structural Basis of Substrate Recognition and Covalent Inhibition of Cdu1 from Chlamydia trachomatis

et al. 2018

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“…FlexX was run in command line mode with a default docking procedure, followed by post-docking optimization. Root mean square deviations were calculated using fconv (G. Neudert and G. Klebe, University of Marburg, 2012), version 1.24 (59).…”

Section: Methodsmentioning

confidence: 99%

Rational Design of Broad Spectrum Antibacterial Activity Based on a Clinically Relevant Enoyl-Acyl Carrier Protein (ACP) Reductase Inhibitor

Schiebel

Chang

Shah

et al. 2014

Journal of Biological Chemistry

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Background:The FabI inhibitor CG400549 is a promising new anti-staphylococcal drug candidate with recently validated human efficacy. Results: We revealed the molecular determinants conferring S. aureus FabI selectivity to rationally design a compound with an improved antibacterial activity spectrum. Conclusion:The 4-pyridone PT166 represents a critical step toward Gram-negative and mycobacterial coverage. Significance: We provide an approach to expand the spectrum of antimicrobial activity.

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“…Analysis of temperature factors was performed with Moleman 45 and fconv. 46 The naming of the protein amino acids was performed according to Bode et al 47 The figures were prepared using PyMOL 0.99. The PDB accession codes of the coordinates and structure factors of all X-ray structures are given in Table 6.…”

Section: Structure Determination and Refinementmentioning

confidence: 99%

Impact of Ligand and Protein Desolvation on Ligand Binding to the S1 Pocket of Thrombin

Biela

Khayat

Tan

et al. 2012

Journal of Molecular Biology

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fconv: format conversion, manipulation and feature computation of molecular data

Abstract: fconv is free software available under GNU General Public License. C++ sources and precompiled executables for LINUX/UNIX, Mac OS and Windows, as well as tutorials are available on http://www.agklebe.de.

Cited by 68 publications

References 9 publications

Structural Basis of Substrate Recognition and Covalent Inhibition of Cdu1 from Chlamydia trachomatis

Structural Basis of Substrate Recognition and Covalent Inhibition of Cdu1 from Chlamydia trachomatis

Rational Design of Broad Spectrum Antibacterial Activity Based on a Clinically Relevant Enoyl-Acyl Carrier Protein (ACP) Reductase Inhibitor

Impact of Ligand and Protein Desolvation on Ligand Binding to the S1 Pocket of Thrombin

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