The program HBAT, is a tool to automate the analysis of potential hydrogen bonds and similar type of weak interactions like halogen bonds and non-canonical π interactions in macromolecular structures, available in Brookhaven Protein Database (PDB) file format. HBAT is written using PERL and TK languages. The program generates an MSOFFICE Excel compatible output file for statistical analysis. HBAT identify potential interactions based on geometrical criteria. A series of analysis reports like frequency tables, geometry distribution tables, furcations list are generated. A user friendly GUI offers freedom to select several parameters and options. Graphviz based visualization of hydrogen bond networks in 2D helps to study the cooperativity and anticooperativity geometry in hydrogen bond. HBAT supports post docking interaction analysis between PDB files for any target/receptor (in PDB files) and docked ligands/poses (in SDF). This tool can be implemented in active site interaction analysis, structure based drug design and molecular dynamics simulations.

Support & Updates: Sorry I hardly have anytime to support this software. Honestly, HBAT software is very much buggy and I am the only person on this earth who can understand the source code. Although I have plans to rewrite the whole package by end of this year.

HBNG is a graph theory based tool for visualization of hydrogen bond network in 2D. Digraphs generated by HBNG facilitate visualization of cooperativity and anticooperativity chains and rings in protein structures. HBNG takes hydrogen bonds list files (output from HBAT, HBEXPLORE, HBPLUS and STRIDE) as input and generates a DOT language script and constructs digraphs using freeware AT and T Graphviz tool. HBNG is useful in the enumeration of favorable topologies of hydrogen bond networks in protein structures and determining the effect of cooperativity and anticooperativity on protein stability and folding. HBNG can be applied to protein structure comparison and in the identification of secondary structural regions in protein structures.

MeltDNA is a tool for DNA hybridization and melting thermodynamics prediction. MeltDNA considers all factors those determine thermodynamic values, such as base composition, NN parameters, salt dependency (Na+ , Mg++ ), internal mismatch, dangling ends , loops etc. To improve NN model based calculations it relies on fusion matrices and these matrices are extensible. Currently MeltDNA predicts ∆ G, ∆ H, ∆ S, Tm, Ta and Extinction coefficient at 260 nm values.

Support & Updates: Again it is a very nice utility. Highly buggy and I can’t support it due to lack of time and resources. Luckily, now there are better web based servers available for DNA hybridization and melting thermodynamics prediction.