Journal of biomolecular Structure & Dynamics Impact Factor & Information

Publisher: Taylor & Francis

Journal description

The Journal of Biomolecular Structure and Dynamics cordially welcomes manuscripts from active investigators in biological structure, dynamics, interactions and expression. The Journal will cover both experimental and theoretical investigations in the area of nucleic acids, nucleotides, proteins, peptides, membranes, polysaccharides and all their components, metal complexes and model systems. The Journal publishes original articles, communications a la express and timely reviews.

Current impact factor: 2.98

Impact Factor Rankings

2015 Impact Factor Available summer 2015
2013 / 2014 Impact Factor 2.983
2010 Impact Factor 4.986
2009 Impact Factor 1.124
2008 Impact Factor 1.289
2007 Impact Factor 1.413
2006 Impact Factor 1.299
2005 Impact Factor 1.43
2004 Impact Factor 1.113
2003 Impact Factor 1.131
2002 Impact Factor 1.009
2001 Impact Factor 1.243
2000 Impact Factor 1.826
1999 Impact Factor 1.407
1998 Impact Factor 1.643
1997 Impact Factor 1.283

Impact factor over time

Impact factor
Year

Additional details

5-year impact 1.15
Cited half-life 0.00
Immediacy index 0.25
Eigenfactor 0.00
Article influence 0.32
Website Journal of Biomolecular Structure & Dynamics website
Other titles Journal of biomolecular structure & dynamics, Journal of biomolecular structure and dynamics
ISSN 1538-0254
OCLC 9688706
Material type Periodical, Internet resource
Document type Journal / Magazine / Newspaper, Internet Resource

Publisher details

Taylor & Francis

  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
  • Conditions
    • Some individual journals may have policies prohibiting pre-print archiving
    • On author's personal website or departmental website immediately
    • On institutional repository or subject-based repository after either 12 months embargo
    • Publisher's version/PDF cannot be used
    • On a non-profit server
    • Published source must be acknowledged
    • Must link to publisher version
    • Set statements to accompany deposits (see policy)
    • The publisher will deposit in on behalf of authors to a designated institutional repository including PubMed Central, where a deposit agreement exists with the repository
    • STM: Science, Technology and Medicine
    • Publisher last contacted on 25/03/2014
    • This policy is an exception to the default policies of 'Taylor & Francis'
  • Classification
    ​ green

Publications in this journal

  • [Show abstract] [Hide abstract]
    ABSTRACT: Sirtuins are NAD+ dependent lysine deacetylases member of the class III HDAC family. These are demonstrated to be therapeutic targets in parasitic diseases like Schistosomiasis. Observations suggested that sirtuin enzyme is necessary for the functionality of fe/male reproductive system, due to which SmSirt2 is treated as a potential therapeutic target. There are no structural and molecular features of SmSirt2 have been reported yet. In this study, homology modeling has been used to determine the three-dimensional features of the SmSITRT2. Further, structure validation has been performed by energy minimization and Ramachandran plot. Validated structures are further subjected to molecular docking and virtual screening to find the best lead molecules for downstream analysis. Ten lead molecules were selected while comparing virtual screening of hSirt2 and SmSirt2 both. These leads are further compared with AKG2 which is known inhibitor of hSirt2 (-8.8kcal/mol). Out of selected 10 leads, four of them (ZINC23995485 (-9.5kcal/mol), ZINC53298162 (-9.4 kcal/mol), ZINC70927268 (-10.0 kcal/mol), ZINC89878705 (-11.2 kcal/mol)) have shown better interaction with SmSirt2, in which ZINC89878705 (-11.2 kcal/mol) shows a more compact packing as compared to AKG2 and rest of ligands. These molecules could be further subject to in vitro study and model of SmSirt2 has been proposed for further structure-based drug design projects concerning sirtuins from S. monsoni.
    Journal of biomolecular Structure & Dynamics 06/2015; DOI:10.1080/07391102.2015.1065205
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    ABSTRACT: Glyoxalase-I (GLO-I) is a component of the ubiquitous detoxification system involved in conversion of methylglyoxal (MG) to D-lactate in the glycolytic pathway. MG toxicity arises from its ability to form advanced glycation end products (AGEs). GLO-I has been reported to be frequently overexpressed in various types of cancer cells. In this study, we performed structure based virtual screening of focussed flavonoids commercial library to identify potential and specific inhibitors of GLO-I. The compounds were ranked based on Glide extra precision docking score and five hits (curcumin, quercetin, morin, naringin and silibinin) were selected on the basis of their interaction with active site amino acid residues of GLO-I. Mixed mode QM/MM calculation was performed on the top scoring hit to ascertain the role of zinc ion in ligand binding. In addition the identified hits were subjected to MM/GBSA binding energy prediction, ADME prediction and similarity studies. The hits were tested in vitro for cell viability, and GLO-I inhibition. Naringin (ST072162) was found to be most potent inhibitor of GLO-I among the identified hits with highest glide XP dock score of -14.906. These findings suggest that naringin could be a new scaffold for designing inhibitors against GLO-I with potential application as anticancer agents.
    Journal of biomolecular Structure & Dynamics 06/2015; DOI:10.1080/07391102.2015.1064830
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    ABSTRACT: The viral immediate-early protein 1 (IE1) is crucial for efficient replication of cytomegalovirus (CMV). A recent crystal structure of the IE1 protein from rhesus CMV revealed that the protein exhibits a novel fold and crystallizes in two slightly different dimeric arrangements. Molecular dynamics simulations and energetic analyses performed in the present study show that both dimers are stable and allowed us to identify a common set of five residues that appear particularly important for dimer formation. These residues are distributed over the entire dimer interface and do not form a typical hot spot for protein interactions. In addition, the dimer interface of IE1 proved to include a high portion of hydrophilic interactions pointing towards the transient nature of dimer formation. Characterization of monomeric and dimeric IE1 revealed three sequentially discontinuous dynamic domains that exhibit correlated motion within the domain and are simultaneously anti-correlated to the adjacent domains. The hinge motions observed between the dynamic domains increase the shape complementarity to the coiled-coiled region of tripartite motif (TRIM) proteins, suggesting that the detected dynamics of IE1 might be physiologically important by enabling a better interaction with its cellular target molecules.
    Journal of biomolecular Structure & Dynamics 06/2015; DOI:10.1080/07391102.2015.1065204
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    ABSTRACT: Drugs from natural resources contribute a great deal as dependable therapeutics against numerous human diseases. An antiviral compound, (5E)-3-(2-aminoethyl)-5-benzylidene-1,3-thiazolidine-2,4-dione (CID:1656714), was examined by us as a dependable substitute for FDA approved non-nucleoside drugs against AIDS (Acquired immunodeficiency syndrome), which is a life-threatening malady caused by HIV (Human Immunodeficiency Virus). Potent inhibition of reverse transcriptase activity (HIV-1RT) is prominent clinically viable strategy for the treatment of AIDS. Modern tools of bioinformatics including molecular docking and simulations were used. Our results demonstrate high binding affinity and non-competitive inhibition of HIV-1RT receptor by (5E)-3-(2-aminoethyl)-5-benzylidene-1,3-thiazolidine-2,4-dione. As compared to other FDA-approved drugs, long de novo simulations and docking study suggest strong binding interactions of this molecule with Asp113, Asp110, Asp185 and Asp186 amino acids, all of which comprise one or the other catalytic pockets of HIV-1RT. These interactions could be critical for potent inhibition of the HIV-1RT receptor. This study thus provides an evidence for consideration of CID: 1656714 as a valuable drug for the treatment and prevention of HIV-associated disorders with low toxicity to normal human cells.
    Journal of biomolecular Structure & Dynamics 06/2015; 33(sup1):124-124.
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    ABSTRACT: Using molecular modelling we have investigated the structure and dynamic properties of epothilone B-tubulin complexes with wild-type and mutated tubulin, aimed at identifying the molecular factors involved in the emergence of drug resistance induced by four protein mutations at Phe270Val, Thr274Ile, Arg282Gln and Gln292Glu. Our results revealed that tubulin mutations render significant changes in the protein conformation in regions involved either in the binding of the ligand or in interdimer contacts that are relevant to the assembly of stable microtubules. In addition, point mutations induce drastic changes in the binding pose of the ligand and in the interaction networks responsible for the epothilone-tubulin association. Large ligands displacements inside the binding pocket and an overall decrease in the strength of drug-receptor polar contacts suggest a looser binding of the ligand in tubulin mutants. These results explain the loss of activity for epothilone B against cancer cells that contain tubulin mutants and provide valuable information to enhance the understanding of the atomic source of epothilones' activity, which can be helpful to conduct further research on the rational design of more potent therapeutic tubulin-binding agents.
    Journal of biomolecular Structure & Dynamics 06/2015; DOI:10.1080/07391102.2015.1063455
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    ABSTRACT: We explore with Molecular modeling, Dynamics simulations and a statistical model, for the ability of Chitosan nanoneedles to be internalized into a model lipid bilayer as a function of their length; keeping in view of their applications in the field of biomedicine for advanced targeted drug delivery. In the present study, we have computationally modeled and studied the structural geometry and the stability of Chitosan Nanoneedles (CNN) formed by 4, 6, and 8 subunits. We reported the molecular surface analysis of the modeled CNN's along with Molecular Dynamic (MD) simulations studies towards revealing the non-invasive cellular internalization potential of these chitosan nanoneedles and a case study has been carried to study the ability of CNN's to translocate silver nanoparticles across membrane. The present results are strongly in support of further exploration of 8 subunits based CNN's for their application as target drug delivery vehicles. The hydrophilicity of the CNN's has been attributed as one of the key factors responsible for the internalization process. Moreover, our MD simulation studies marched the ability of Chitosan Nanoneedles to translocate silver nanoparticles through biological membrane in a similar manner that resembles cell-penetrating peptides.
    Journal of biomolecular Structure & Dynamics 06/2015; DOI:10.1080/07391102.2015.1062803
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    ABSTRACT: Targeting, silencing or imaging miRNA molecules have been considered promising methods for fighting cancer at the molecular level. microRNAs (miRNAs) are small noncoding RNA molecules (~22 nucleotides) that regulate gene expression at the post-transcriptional level. miR-10b has been found over-expressed in metastatic breast cancer. Inhibiting the functions of miR-10b using single stranded synthetic anti-sense Locked Nucleic Acid (LNA) molecules has shown effective therapeutic results for metastatic breast cancer. The objective of this study was to understand the interaction between miR-10b with its complementary natural or unnatural anti-sense strands using two-dimensional graphene (nGO) and Molybdenum disulfide (MoS2). Here we used nGO and MoS2 to investigate the interaction between an LNA modified antisense oligonucleotide and its target oncomiR (miR-10b). In this study, nGO and MoS2 serve as a firm nano-platform for nucleic acids with or without base modification, while providing rich kinetic and spectroscopic information about their interaction. Moreover, we were able to validate the stability of the oligonucleotide and nGO or MoS2 nanoassemblies (nGO/ssDNA or MoS2/ssDNA) at different temperatures. In conclusion, we demonstrate that two-dimensional nanomaterials serve as a superb nano-platform for monitoring nucleic acid interactions, which have essential implications in miRNA imaging and therapeutic technologies. We were able to observe the similarities and differences in interactions between miR-10b and its LNA or DNA complementary strands using rapid quenching and adsorbing properties of nGO and MoS2. The stability of the nGO/ssDNA or MoS2/ssDNA nanoassemblies in a wide range of temperatures suggests that it is an attractive nanomaterial for monitoring hybridization and de-hybridization of oligonucleotides.
    Journal of Biomolecular Structure and Dynamics (Albany 2015: The 19th Conversation), Albany, NY; 06/2015
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    ABSTRACT: The interaction of the plant alkaloid aristololactam-β-D-glucoside (ADG) and the anticancer agent daunomycin (DAN) with Human hemoglobin was studied by different spectroscopic and calorimetric methods. The binding affinity values of ADG and DAN estimated from spectroscopic experiments were 3.79 x 10(4) and 6.68 x 10(4) M(-1), respectively. From circular dichroism, 3D fluorescence and FTIR studies it was observed that DAN induced stronger conformational changes than ADG in the protein. From synchronous fluorescence spectroscopy results, a pronounced shift in the maximum emission wavelength of tyrosine residues was observed in both cases suggesting that the drugs changed the polarity around tyrosine residues with marginal change around the tryptophan residues. The thermodynamics of the binding interaction analyzed using microcalorimetry presented single binding events that were exothermic in nature in both cases. The binding was driven by large positive molar entropy changes with small favorable enthalpy contributions. Negative heat capacity changes in both cases are correlated to the involvement of significant hydrophobic forces in the complexation process. The affinity of DAN to Hb was higher than that of ADG.
    Journal of biomolecular Structure & Dynamics 06/2015; DOI:10.1080/07391102.2015.1055304
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    ABSTRACT: The interaction of native fish salmon DNA (FS-DNA) with [Eu(bpy)3Cl2(H2O)]Cl, where bpy is 2,2'-bipyridine, is studied at physiological pH in Tris-HCl buffer by spectroscopic methods, viscometric techniques as well as circular dichroism (CD). These experiments reveal that Eu(III) complex has interaction with FS-DNA. Moreover, binding constant and binding site size have been determined. The value of Kb has been defined 2.46 ± .02 × 10(5) M(-1). The thermodynamic parameters are calculated by Van't Hoff equation, the results show that the interaction of the complex with FS-DNA is an entropically driven phenomenon. CD spectroscopy followed by viscosity as well as fluorescence and UV--Vis measurements indicate that the complex interacts with FS-DNA via groove binding mode. Also, the synthesized Eu(III) complex has been screened for antimicrobial activities.
    Journal of biomolecular Structure & Dynamics 06/2015; DOI:10.1080/07391102.2015.1048481
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    ABSTRACT: Cyclophilins (CyPs) are enzymes involved in protein folding. In Trypanosoma cruzi (T. cruzi), the most abundantly expressed CyP is the isoform TcCyP19. It has been shown that TcCyP19 is inhibited by the immunosuppressive drug cyclosporin A (CsA) and analogs, which also proved to have potent trypanosomicidal activity in vitro. In this work, we continue and expand a previous study on the molecular interactions of CsA, and a set of analogs modeled in complexes with TcCyP19. The modeled complexes were used to evaluate binding free energies by molecular dynamics (MD), applying the Linear Interaction Energy (LIE) method. In addition, putative binding sites were identified by molecular docking. In our analysis, the binding free energy calculations did not correlate with experimental data. The heterogeneity of the non-bonded energies and the variation in the pattern of hydrogen bonds suggest that the systems may not be suitable for the application of the LIE method. Further, the docking calculations identified two other putative binding sites with comparable scoring energies to the active site, a fact that may also explain the lack of correlation found. Kinetic experiments are needed to confirm or reject the multiple binding sites hypothesis. In the meantime, MD simulations at the alternative sites, employing other methods to compute binding free energies, might be successful at finding good correlations with the experimental data.
    Journal of biomolecular Structure & Dynamics 06/2015; DOI:10.1080/07391102.2015.1038584
  • Journal of biomolecular Structure & Dynamics 06/2015;
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    ABSTRACT: The infamous chronic neurodegenerative disease, Alzheimer's, that starts with short term memory loss and eventually leads to gradual bodily function decline which has been attributed to the deficiency in brain neurotransmitters, acetylcholine and butylcholine. As a matter of fact, design of compounds that can inhibit cholinesterases activities (acetylcholinesterase (AChE) and butylcholinesterase (BChE)) has been introduced as an efficient method to treat Alzheimer's. Among proposed compounds, bis(7)tacrine (B7T) is recognized as a noteworthy suppressor for Alzheimer's disease. Recently a new analogue of bis(7)tacrine, cystamine-tacrine dimer is offered as an agent to detain Alzheimer's complications, even better than the parent compound. In this study, classical molecular dynamic simulations has been employed to take a closer look into the modes of interactions between the mentioned ligands and both cholinesterase enzymes. According to our obtained results, the structural differences in the target enzymes active sites result in different modes of interactions and inhibition potencies of the ligands against both enzymes. The obtained information can help to investigate those favorable fragments in the studied ligands skeletons that have risen potency of the analogue in comparison to the parent compound to design more potent multi target ligands to heal Alzheimer's disease.
    Journal of biomolecular Structure & Dynamics 06/2015; DOI:10.1080/07391102.2015.1057526