02219nas a2200157 4500008004100000022001400041245009300055210006900148260007100217300001200288490000700300520157600307100003301883700002001916856012501936 2005 eng d a1549-959600aEncoding and decoding graphical chemical structures as two-dimensional (PDF417) barcodes0 aEncoding and decoding graphical chemical structures as twodimens a1155 16TH ST, NW, WASHINGTON, DC 20036 USAbAMER CHEMICAL SOCcMAY a572-5800 v453 a

A wide range of molecular representations exist today, ranging from human-readable structural diagrams over line notations such as Wiswesser Line Notation (WLN) and SMILES to several dozen computer-readable file formats. Still, to encode molecular structures in a computer-readable way for inputting structures in computer systems those formats are not the method of choice since they are not easily and faultlessly readable via optical recognition. In the present study a two-dimensional (PDF417) barcode representation of molecular structures in SMILES format is explored that enables the user to read and input molecular structures into computer systems in a fully automated fashion. A Lempel-Ziv-Welch (LZW) based compressed version of SMILES is suggested for cases where the size of the structure exceeds the storage capacity of PDF417 barcodes. Alternatively, the compact ACS format may be employed as a structural representation. The input via barcodes is fast, practically error free due to the 2D barcodes used which employ error correction and fully automatic. A Web application interface is developed which is able to interpret these barcodes and export them as optimized 3D chemical structures. Applications of this representation range from keeping automated storage systems to Web-based tracking systems of molecular samples. The National Chemical Laboratory, Pune, employs 2D barcode encoded structures for in-house repository management, where barcodes can also be used for querying the database for similar or substructures of the query structure.

1 aKarthikeyan, Muthukumarasamy1 aBender, Andreas uhttps://library.ncl.res.in/content/encoding-and-decoding-graphical-chemical-structures-two-dimensional-pdf417-barcodes-003557nas a2200157 4500008004100000245008600041210006900127260000800196300001200204490000700216520299400223100001803217700001503235700003303250856011603283 2019 eng d00aExploring energy profiles of protein-protein interactions (PPIs) Using DFT method0 aExploring energy profiles of proteinprotein interactions PPIs Us cJUN a670-6770 v163 a

Background: Large-scale energy landscape characterization of protein-protein interactions (PPIs) is important to understand the interaction mechanism and protein-protein docking methods. The experimental methods for detecting energy landscapes are tedious and the existing computational methods require longer simulation time.

Objective: The objective of the present work is to ascertain the energy profiles at the interface regions in a rapid manner to analyze the energy landscape of protein-protein interactions

Methods: The atomic coordinates obtained from the X-ray and NMR spectroscopy data are considered as inputs to compute cumulative energy profiles for experimentally validated protein-protein complexes. The energies computed by the program were comparable to the standard molecular dynamics simulations.

Results: The PPI Profiler not only enables rapid generation of energy profiles but also facilitates the detection of hot spot residue atoms involved therein.

Conclusion: The hotspot residues and their computed energies matched with the experimentally determined hot spot residues and their energies which correlated well by employing the MM/GBSA method. The proposed method can be employed to scan entire proteomes across species at an atomic level to study the key PPI interactions.

1 aBapat, Sanket1 aVyas, Renu1 aKarthikeyan, Muthukumarasamy uhttps://library.ncl.res.in/content/exploring-energy-profiles-protein-protein-interactions-ppis-using-dft-method