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CAVER: a new tool to explore routes from protein clefts, pockets and cavities
An algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent is developed and implemented for the CAVER program. Expand
Structures and mechanisms of glycosyltransferases.
The 3D-Glycosyltransferase database is created to gather structural information concerning this class of enzymes and to accommodate the growing number of crystal structures. Expand
MOLE 2.0: advanced approach for analysis of biomacromolecular channels
Estimated physicochemical properties of the identified channels in the selected biomacromolecules corresponded well with the known functions of the respective channels, and may provide useful information about the potential functions of identified channels. Expand
MOLE: a Voronoi diagram-based explorer of molecular channels, pores, and tunnels.
Tests on a wide variety of biomolecular systems including gramicidine, acetylcholinesterase, cytochromes P450, potassium channels, DNA quadruplexes, ribozymes, and the large ribosomal subunit have demonstrated that the MOLE algorithm performs well and is a powerful tool for exploring large molecular channels, complex networks of channels, and molecular dynamics trajectories. Expand
Protein Data Bank: the single global archive for 3D macromolecular structure data
  • Stephen K Helen M Charmi Chunxiao Li Luigi Di Cole Jose M Burley Berman Bhikadiya Bi Chen Costanzo Christie , S. Burley, +80 authors Y. Ioannidis
  • Biology, Medicine
  • Nucleic acids research
  • 24 October 2018
Impacts of the recently developed universal wwPDB OneDep deposition/validation/biocuration system and various methods-specific ww PDB Validation Task Forces on improving the quality of structures and data housed in the PDB Core Archive are described together with current challenges and future plans. Expand
MOLEonline 2.0: interactive web-based analysis of biomacromolecular channels
A web-based interactive MOLEonline 2.0 application for the analysis of access/egress paths to interior molecular voids and 3D graphical representation of the channel, its profile accompanied by a list of lining residues and also its basic physicochemical properties is introduced. Expand
LiteMol suite: interactive web-based visualization of large-scale macromolecular structure data
We present the LiteMol suite, a tool for visualizing large macromolecular structure data sets that is freely available at https://www.litemol.org.
PDBe: improved findability of macromolecular structure data in the PDB
The enrichment of data at PDBe is detailed, including mapping of RNA structures to Rfam, and identification of molecules that act as cofactors and an advanced search facility with ∼100 data categories and sequence searches. Expand
Formation pathways of a guanine-quadruplex DNA revealed by molecular dynamics and thermodynamic analysis of the substates.
The simulations suggest that "cross-like" two-stranded assemblies may serve as nucleation centers in the initial formation of parallel stranded G-DNA quadruplexes, proceeding through a series of rearrangements involving trapping of cations, association of additional strands, and progressive slippage of strands toward the full stem. Expand
Molecular dynamics simulations of Guanine quadruplex loops: advances and force field limitations.
The study provides, within the approximations of the applied all-atom additive force field, a qualitatively complete analysis of the available loop conformational space and the optimal diagonal and lateral loop arrangements appear to be close in energy although a proper inclusion of the loop monovalent cations could stabilize the diagonal architecture. Expand