PHYSICO: An UNIX based Standalone Procedure for Computation of Individual and Group Properties of Protein Sequences

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Specific electrostatics (i.e. salt-bridge) includes both local and non-local interactions that contribute to the overall stability of proteins. It has been shown that a salt-bridge could either be buried or exposed, networked or isolated, hydrogen-bonded or nonhydrogen bonded, in secondary-structure or in coil, formed by single or multiple bonds. Further it could also participates either in intra- or inter-dipole interactions with preference in orientation either for basic residue at N-terminal (orientation-I) or acidic residue at N-terminal (orientation-II). In this context SBION2 is unique in that it reports above mentioned binary items in excel format along with details on intra and inter-dipole interactions and orientations. These results are suitable for post run statistical analyses involving large datasets. Reports are also made on protein-protein interactions, intervening residue distances and general residue specific salt-bridge details. A ready to use compact supplementary table is also produced. The program runs in three alternative modes. Each mode works on any number of structure files with any number of chains at any given atomic distance of ion-pair. Thus SBION2 provides intricate details on salt-bridges and finds application in structural bioinformatics.AvailabilitySBION2 is freely available at http://sourceforge.net/projects/sbion2/ for academic users

“…SBION2, like our earlier developments [ 1 , 4 ], is meant for automated analysis of single or multiple input(s). The program possesses many new features over the existing ones.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

SBION2: Analyses of Salt Bridges from Multiple Structure Files, Version 2

Gupta¹,

Nayek²,

Banerjee³

et al. 2015

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“…We are developing web interface to integrate SBION and other tools such as PHYSICO [9] developed in our lab, within a unique web service.…”

Section: Caveats and Future Developmentmentioning

confidence: 99%

SBION: A Program for Analyses of Salt-Bridges from Multiple Structure Files

Gupta¹,

Mondal²,

Mondal³

et al. 2014

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Salt-bridge and network salt-bridge are specific electrostatic interactions that contribute to the overall stability of proteins. In hierarchical protein folding model, these interactions play crucial role in nucleation process. The advent and growth of protein structure database and its availability in public domain made an urgent need for context dependent rapid analysis of salt-bridges. While these analyses on single protein is cumbersome and time-consuming, batch analyses need efficient software for rapid topological scan of a large number of protein for extracting details on (i) fraction of salt-bridge residues (acidic and basic). (ii) Chain specific intra-molecular salt-bridges, (iii) inter-molecular salt-bridges (protein-protein interactions) in all possible binary combinations (iv) network salt-bridges and (v) secondary structure distribution of salt-bridge residues. To the best of our knowledge, such efficient software is not available in public domain. At this juncture, we have developed a program i.e. SBION which can perform all the above mentioned computations for any number of protein with any number of chain at any given distance of ion-pair. It is highly efficient, fast, error-free and user friendly. Finally we would say that our SBION indeed possesses potential for applications in the field of structural and comparative bioinformatics studies.AvailabilitySBION is freely available for non-commercial/academic institutions on formal request to the corresponding author (akbanerjee@biotech.buruniv.ac.in).

“…Further, sharing of same websoftware by worldwide users might cause lower processivity. While PHYSICO [ 10 ], in contrast performs batch analyses for PWS properties, their ranges are still less exhaustive. Now the later to serve better, an upgraded version seems urgent such that users i] could relish the flexibility in setting relevant inputparameters, ii] could procure additional outputs on windowdependent profiles for RAW-FASTA, pI-profiles and items in similar kind of output as PHYSICO that contains novel reports on substitution-based positional as well as BLOCK specific diversity and conservation, iii] can access detailed documentation on principle and methodologies used in the program.…”

Section: Introductionmentioning

confidence: 99%

PHYSICO2: an UNIX based standalone procedure for computation of physicochemical, window-dependent and substitution based evolutionary properties of protein sequences along with automated block preparation tool, version 2

Banerjee¹,

Gupta²,

Nayek³

et al. 2015

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Automated genome sequencing procedure is enriching the sequence database very fast. To achieve a balance between the entry of sequences in the database and their analyses, efficient software is required. In this end PHYSICO2, compare to earlier PHYSICO and other public domain tools, is most efficient in that it i] extracts physicochemical, window-dependent and homologousposition-based-substitution (PWS) properties including positional and BLOCK-specific diversity and conservation, ii] provides users with optional-flexibility in setting relevant input-parameters, iii] helps users to prepare BLOCK-FASTA-file by the use of Automated Block Preparation Tool of the program, iv] performs fast, accurate and user-friendly analyses and v] redirects itemized outputs in excel format along with detailed methodology. The program package contains documentation describing application of methods. Overall the program acts as efficient PWS-analyzer and finds application in sequence-bioinformatics.AvailabilityPHYSICO2: is freely available at http://sourceforge.net/projects/physico2/ along with its documentation at https://sourceforge.net/projects/physico2/files/Documentation.pdf/download for all users.