COILCHECK: An Interactive Server for the Analysis of Interface Regions in Coiled Coils

Sowdhamini, Ramanathan; Alva, Vikram; devi, D. Parimala

doi:10.2174/092986608783330314

Cited by 21 publications

(13 citation statements)

References 14 publications

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“…One popular manner of associating strength or stability is to attribute psuedoenergies to the system of interest [35]. The potential energy due to intermolecular interactions at coiled-coils could be viewed as a sum of individual components such as van der Waals and electrostatic intermolecular interactions, as described in our in-house program COILCHECK [36]. The gap between sequence, structure and stability of a coiled-coil molecule is efficiently bridged by the COILCHECK program, which acts as a promising tool to identify and compare weak and strong regions within coiled-coil structures.…”

Section: Introductionmentioning

confidence: 99%

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Structural attributes for the recognition of weak and anomalous regions in coiled-coils of myosins and other motor proteins

et al. 2012

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BackgroundCoiled-coils are found in different proteins like transcription factors, myosin tail domain, tropomyosin, leucine zippers and kinesins. Analysis of various structures containing coiled-coils has revealed the importance of electrostatic and hydrophobic interactions. In such domains, regions of different strength of interactions need to be identified since they could be biologically relevant.FindingsWe have updated our coiled-coil validation webserver, now called COILCHECK+, where new features were added to efficiently identify the strength of interaction at the interface region and measure the density of charged residues and hydrophobic residues. We have examined charged residues and hydrophobic ladders, using a new algorithm called CHAHO, which is incorporated within COILCHECK + server. CHAHO permits the identification of spatial charged residue patches and the continuity of hydrophobic ladder which stabilizes and destabilizes the coiled-coil structure.ConclusionsThe availability of such computational tools should be useful to understand the importance of spatial clustering of charged residues and the continuity of hydrophobic residues at the interface region of coiled-coil dimers. COILCHECK + is a structure based tool to validate coiled-coil stability; it can be accessed at http://caps.ncbs.res.in/coilcheckplus.

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Section: Introductionmentioning

confidence: 99%

“…The magnitude and nature of the interaction between the coiled-coil dimer is provided as energy per residue in COILCHECK (for details on COILCHECK method and energy range please see [36]). Since then, the program has been updated to include new features and we refer to the new version of webserver as ‘COILCHECK+’.…”

Section: Introductionmentioning

confidence: 99%

Structural attributes for the recognition of weak and anomalous regions in coiled-coils of myosins and other motor proteins

et al. 2012

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“…A Coil check online tool was used to determine the electrostatic energy, Van der waals energy and total stabilizing energy between the complexes [63]. A proteins, Interfaces, Structures and Assemblies (PDBePISA) interactive tool was used to find out the total accessible surface area, buried area, solvation free energy gain upon complex formation, free energy of assembly dissociation, P-value for interface specificity, the number of salt bridges and the number of hydrogen bonds across the interface [64].…”

Section: Methodsmentioning

confidence: 99%

Identification of Biomarkers for Resistance to Fusarium oxysporum f. sp. cubense Infection and in Silico Studies in Musa paradisiaca Cultivar Puttabale through Proteomic Approach

et al. 2016

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Panama wilt caused by Fusarium oxysporum f. sp. cubense (Foc) is one of the major disease constraints of banana production. Previously, we reported the disease resistance Musa paradisiaca cv. puttabale clones developed from Ethylmethanesulfonate and Foc culture filtrate against Foc inoculation. Here, the same resistant clones and susceptible clones were used for the study of protein accumulation against Foc inoculation by two-dimensional gel electrophoresis (2-DE), their expression pattern and an in silico approach. The present investigation revealed mass-spectrometry identified 16 proteins that were over accumulated and 5 proteins that were under accumulated as compared to the control. The polyphosphoinositide binding protein ssh2p (PBPssh2p) and Indoleacetic acid-induced-like (IAA) protein showed significant up-regulation and down-regulation. The docking of the pathogenesis-related protein (PR) with the fungal protein endopolygalacturonase (PG) exemplify the three ionic interactions and seven hydrophobic residues that tends to good interaction at the active site of PG with free energy of assembly dissociation (1.5 kcal/mol). The protein-ligand docking of the Peptide methionine sulfoxide reductase chloroplastic-like protein (PMSRc) with the ligand β-1,3 glucan showed minimum binding energy (−6.48 kcal/mol) and docking energy (−8.2 kcal/mol) with an interaction of nine amino-acid residues. These explorations accelerate the research in designing the host pathogen interaction studies for the better management of diseases.

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“…This is to avoid steric clashes and stabilise the complex as a whole. Our program CoilCheck [16] was employed to obtain the Van der Waals interaction energy between the two chains of the protein complex. This energy was used as a measure of the short contacts present at the interface.…”

Section: Methodsmentioning

confidence: 99%

Structural Interface Parameters Are Discriminatory in Recognising Near-Native Poses of Protein-Protein Interactions

2014

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Interactions at the molecular level in the cellular environment play a very crucial role in maintaining the physiological functioning of the cell. These molecular interactions exist at varied levels viz. protein-protein interactions, protein-nucleic acid interactions or protein-small molecules interactions. Presently in the field, these interactions and their mechanisms mark intensively studied areas. Molecular interactions can also be studied computationally using the approach named as Molecular Docking. Molecular docking employs search algorithms to predict the possible conformations for interacting partners and then calculates interaction energies. However, docking proposes number of solutions as different docked poses and hence offers a serious challenge to identify the native (or near native) structures from the pool of these docked poses. Here, we propose a rigorous scoring scheme called DockScore which can be used to rank the docked poses and identify the best docked pose out of many as proposed by docking algorithm employed. The scoring identifies the optimal interactions between the two protein partners utilising various features of the putative interface like area, short contacts, conservation, spatial clustering and the presence of positively charged and hydrophobic residues. DockScore was first trained on a set of 30 protein-protein complexes to determine the weights for different parameters. Subsequently, we tested the scoring scheme on 30 different protein-protein complexes and native or near-native structure were assigned the top rank from a pool of docked poses in 26 of the tested cases. We tested the ability of DockScore to discriminate likely dimer interactions that differ substantially within a homologous family and also demonstrate that DOCKSCORE can distinguish correct pose for all 10 recent CAPRI targets.

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COILCHECK: An Interactive Server for the Analysis of Interface Regions in Coiled Coils

Cited by 21 publications

References 14 publications

Structural attributes for the recognition of weak and anomalous regions in coiled-coils of myosins and other motor proteins

Structural attributes for the recognition of weak and anomalous regions in coiled-coils of myosins and other motor proteins

Identification of Biomarkers for Resistance to Fusarium oxysporum f. sp. cubense Infection and in Silico Studies in Musa paradisiaca Cultivar Puttabale through Proteomic Approach

Structural Interface Parameters Are Discriminatory in Recognising Near-Native Poses of Protein-Protein Interactions

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