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 0739-1102
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: 6-Thiogunine (6-TG) is an antineoplastic, nucleobase guanine, purine analogue drug belongs to thiopurine drug-family of anti-metabolites. In the present study we have report an experimental approach towards interaction mechanism of 6-TG with human serum albumin (HSA) and examine the chemical stability of HSA in the presence of denaturants such as guanidine hydrochloride (GdnHCl) and urea. Interaction of 6-TG with HSA has been studies by various spectroscopic and spectropolarimeteric methods to investigate what short of binding occurs at physiological conditions. 6-TG binds in the hydrophobic cavity of subdomain IIA of HSA by static quenching mechanism which induces conformation alteration in the protein structure. That helpful for further study of denaturation process where conformational alteration in secondary structures causes unfolding of protein that also responsible for severance of domain III from rest of the protein part. We have also performed molecular simulation and molecular docking study in the presence of denaturating agents to determine the binding property of 6-TG and the effect of denaturating agents on the structural activity of HSA. We had found that GdnHCl is more effective denaturating agent in compare to urea. Hence, this study provides straight evidence of the binding mechanism of 6-TG with HSA and the formation of intermediate or unfolding transition that causes unfolding of HSA.
    Journal of biomolecular Structure & Dynamics 05/2015; DOI:10.1080/07391102.2015.1054433
  • [Show abstract] [Hide abstract]
    ABSTRACT: The estimation of atomic partial charges of the small molecules to calculate molecular interaction fields (MIFs) is an important process in field-based quantitative structure-activity relationship (QSAR). Several studies showed the influence of partial charge schemes that drastically affects the prediction accuracy of the QSAR model and focused on the selection of appropriate charge models that provide highest cross-validated correlation coefficient (r2cv or q2) to explain the variation in chemical structures against biological endpoints. The present study shift this focus in a direction to understand the molecular regions deemed to explain SAR in various charge models and recognize a consensus picture of activity-correlating molecular regions. We selected eleven diverse dataset and developed MIF-based QSAR models using various charge schemes including Gasteiger-Marsili, Del Re, Merck Molecular Force Field, Hückel, Gasteiger-Hückel and Pullman. The generalized resultant QSAR models were then compared with Open3DQSAR model to interpret the MIF descriptors decisively. We suggest the regions of activity contribution or optimization can be effectively determined by studying various charge-based models to understand SAR precisely.
    Journal of biomolecular Structure & Dynamics 04/2015; DOI:10.1080/07391102.2015.1044474
  • [Show abstract] [Hide abstract]
    ABSTRACT: Raman spectroscopy has been used to study the eigenvectors and eigenvalues of the vibrational modes of crystalline cytidine at 295 K and high pressures by evaluating the logarithmic derivative of the vibrational frequency ω with respect to pressure P: . Crystalline samples of molecular materials have strong intramolecular bonds and weak intermolecular bonds. This hierarchy of bonding strengths causes the vibrational optical modes localized within a molecular unit (“internal” modes) to be relatively high in frequency while the modes in which the molecular units vibrate against each other (“external” modes) have relatively low frequencies. The value of the logarithmic derivative is a useful diagnostic probe of the nature of the eigenvector of the vibrational modes because stretching modes (which are predominantly internal to the molecule) have low logarithmic derivatives while external modes have higher logarithmic derivatives. In crystalline cytidine, the modes at 85.8, 101.4, and 110.6 cm−1 are external in which the molecules of the unit cell vibrate against each other in either translational or librational motions (or some linear combination thereof). All of the modes above 320 cm−1 are predominantly internal stretching modes. The remaining modes below 320 cm−1 include external modes and internal modes, mostly involving either torsional or bending motions of groups of atoms within a molecule.
    Journal of biomolecular Structure & Dynamics 04/2015; 33(4). DOI:10.1080/07391102.2014.915763
  • [Show abstract] [Hide abstract]
    ABSTRACT: The bulk of strong nucleosomes (SNs, with visibly periodic DNA sequences) are described by consensus pattern of 5 or 6 base runs of purines alternating with similar runs of pyrimidines - RR/YY SNs. Yet, the strongest known nucleosome positioning sequence, the 601 clone of Lowary and Widom, is rather periodic repetition of TA dinucleotides following one another every 10 bases. We located "601"-like TA-periodic sequences in the genome of A. thaliana. Several families of such sequences are discovered repeating almost exclusively in centromeres. Thus, while A. thaliana SNs of RR/YY type have strong affinity to pericentromeric regions, as it has been previously found, the SNs of TA-periodic type concentrate rather in centromeres.
    Journal of biomolecular Structure & Dynamics 03/2015; DOI:10.1080/07391102.2015.1028450
  • [Show abstract] [Hide abstract]
    ABSTRACT: The "stem cells" are commonly defined as "cells capable of self-renewal through replication and differentiating into specific lineages". The mammary gland contains functional stem/progenitor cells. The current study was planned with the objectives to study the differentiation dynamics of Korean Holstein mammary epithelial stem cells (KHMESCs) under the optimum culture conditions. Lineage negative KHMESCs isolated from mammary tissue of lactating cows have shown the typical differentiation dynamics with formation of lobulo-alveolar structures in in vitro culture. This suggests the existence of bipotential mammary epithelial stem cells in the mammary gland. The strong mRNA expression of pluripotency factors indicates stemness, whereas expression of milk protein genes and epithelial cell-specific gene indicate their differentiation capabilities. Further, immunostaining results have shown the differentiation capabilities of KHMESCs into both luminal and basal lineages under the extracellular matrix (ECM, matrigel) free environment. However, under matrigel, the differentiation process was comparatively higher than without matrigel. Immunostaining results also suggested that differentiated cells could secrete milk proteins such as β-casein. To our knowledge, these data represent the first report on the differentiation dynamics and establishment of mammary epithelial stem cells from Korean Holstein with typical stemness properties. It was observed that isolated KHMESCs had normal morphology, growth pattern, differentiation ability, cytogenetic and secretory activity even without ECM. Therefore, it is concluded that established KHMESCs could be used for further studies on Korean Holstein dairy cows related to lactation studies, as non-GMO animal bioreactors and stem cell-based management of bovine mastitis including post-mastitis damage.
    Journal of biomolecular Structure & Dynamics 03/2015; DOI:10.1080/07391102.2014.1003197
  • [Show abstract] [Hide abstract]
    ABSTRACT: Molecular dynamics (MD) simulation methods have seen significant improvement since their inception in the late 1950's (Alder, 1959). Constraints of simulation size and duration that once impeded the field have lessened with the advent of better algorithms, faster processors, and parallel computing. All-atom simulations once limited to hundreds of atoms on nanosecond time-scale (Brooks et al., 2009; Phillips et al., 2005) are now, in comparable amounts of computer time, handling many thousands of atoms in the microsecond regime. (Harvey, Giupponi, & Fabritiis, 2009) With newer techniques and hardware available, MD simulations of more biologically relevant timescales can now sample a broader range of conformational and dynamical changes including rare events. One concern in the literature has been under which circumstances it is sufficient to perform many shorter timescale simulations and under which circumstances fewer longer simulations are necessary. Herein, our simulations of the zinc-finger NEMO (2JVX) using multiple simulations of length 15, 30, 1000, and 3000ns are analyzed to provide clarity on this point.
    Journal of biomolecular Structure & Dynamics 03/2015; DOI:10.1080/07391102.2015.1015168
  • [Show abstract] [Hide abstract]
    ABSTRACT: There were 1765 contacts identified between DNA nucleobases or deoxyribose and cyclic (W, H, F, Y) or acyclic (R, E, D) amino acids in 672 X-ray structures of DNA-protein complexes. In this first study to compare π-interactions between the cyclic and acyclic amino acids, visual inspection was used to categorize amino acid interactions as nucleobase π-π (according to biological edge) or deoxyribose sugar-π (according to sugar edge). Overall, 54% of contacts are nucleobase π-π interactions, which involve all amino acids, but are more common for Y, F, and R, and involve all DNA nucleobases with similar frequencies. Among binding arrangements, cyclic amino acids prefer more planar (stacked) π-systems than the acyclic counterparts. Although sugar-π interactions were only previously identified with the cyclic amino acids and were found to be less common (38%) than nucleobase-cyclic amino acid contacts, sugar-π interactions are more common than nucleobase π-π contacts for the acyclic series (61% of contacts). Similar to DNA-protein π-π interactions, sugar-π contacts most frequently involve Y and R, although all amino acids adopt many binding orientations relative to deoxyribose. These DNA-protein π-interactions stabilize biological systems, by up to approximately -40 kJ mol(-1) for neutral nucleobase or sugar-amino acid interactions, but up to approximately -95 kJ mol(-1) for positively or negatively charged contacts. The high frequency and strength, despite variation in structure and composition, of these π-interactions point to an important function in biological systems.
    Journal of biomolecular Structure & Dynamics 02/2015; DOI:10.1080/07391102.2015.1013157
  • [Show abstract] [Hide abstract]
    ABSTRACT: The melting transition of DNA-ligand complexes, allowing for two binding mechanisms to different DNA conformations is treated theoretically. The obtained results express the behavior of the experimentally measurable quantities, degree of denaturation, and concentrations of bound ligands on the temperature. The range of binding parameters is obtained, where denaturation curves become multiphasic. The possible application to the nanocomposites crystallization is discussed.
    Journal of biomolecular Structure & Dynamics 02/2015; DOI:10.1080/07391102.2015.1010584
  • [Show abstract] [Hide abstract]
    ABSTRACT: In order to contribute to the structural basis for rational design of calmodulin (CaM) inhibitors, we analyzed the interaction of CaM with 14 classic antagonists and two compounds that do not affect CaM, using docking and molecular dynamics (MD) simulations, and the data were compared to available experimental data. The Ca(2+)-CaM-ligands complexes were simulated 20 ns, with CaM starting in the "open" and "closed" conformations. The analysis of the MD simulations provided insight intro the conformational changes undergone by CaM during its interaction with these ligands. Theses simulations were used to predict the binding free energies (∆G) from their ∆H and ∆S contributions, giving useful information about CaM-ligand binding thermodynamics. The ∆G predicted for the CaM's inhibitors correlated well with available experimental data as the r(2) obtained was 0.76 and 0.82 for the group of xanthones. Additionally, valuable information is presented here: I) CaM has two preferred ligand binding sites in the open conformation known as site 1 and 4, II) CaM can bind ligands of diverse structural nature, III) the flexibility of CaM is reduced by the union of its ligands, leading to a reduction in the Ca(2+)-CaM entropy, IV) enthalpy dominates the molecular recognition process in the system Ca(2+)-CaM-ligand, and V) the ligands making more extensive contact with the protein have higher affinity for Ca(2+)-CaM. Despite their limitations, docking and MD simulations in combination with experimental data, continue to be excellent tools for research in pharmacology, towards a rational design of new drugs.
    Journal of biomolecular Structure & Dynamics 02/2015; DOI:10.1080/07391102.2015.1022225
  • [Show abstract] [Hide abstract]
    ABSTRACT: The combination of several drugs is necessary, especially during long-term therapy. A competitive binding of the drugs can cause a decrease in the amount of drugs actually bound to the protein and increase the biologically active fraction of the drug. Here, the interaction between 4,4'-Diisothiocyano-2,2'-stilbenedisulfonic acid (DIDS) and 2,4-Dinitrophenol (DNP) with Hemoglobin (Hb) was investigated by different spectroscopic and molecular modeling techniques. Fluorescence analysis was used to estimate the effect of the DIDS and DNP on Hb as well as to define the binding properties of binary and ternary complexes. The distance r between donor and acceptor was obtained by the FRET and found to be 2.25 and 2.13 nm for DIDS and DNP in binary and 2.08 and 2.07 nm for (Hb-DNP) DIDS and (Hb-DIDS) DNP complexes in ternary systems, respectively. Time-resolved fluorescence spectroscopy confirmed static quenching for Hb in the presence of DIDS and DNP in both systems. Furthermore, an increase in ellipticity values of Hb upon interaction with DIDS and DNP showed secondary structural changes of protein that determine to disrupt of hydrogen bonds and electrostatic interactions. Our results showed that the Hb destabilize in the presence of DIDS and DNP. Molecular modeling of the possible binding sites of DIDS and DNP in binary and ternary systems in Hb confirmed the experimental results.
    Journal of biomolecular Structure & Dynamics 02/2015; DOI:10.1080/07391102.2015.1009946
  • [Show abstract] [Hide abstract]
    ABSTRACT: Sterol 24-C methyltransferase (SMT) plays a major role during the production of steroids, especially in the biosynthesis of ergosterol, which is the major membrane sterol in leishmania parasite, and the etiological basis of leishmaniasis. Mechanism-based inactivators bind irreversibly to SMT and interfere with its activity to provide leads for the design of antileishmanial inhibitors. In this study, computational methods are used for studying enzyme-inhibitor interactions. fifty-seven mechanism-based inactivators are docked using 3 docking/scoring approaches (FRED, GoldScore, and ChemScore). A consensus is generated from the results of different scoring functions which are also validated with already reported experimental values. The most active compound thus obtained is subjected to molecular dynamics simulation of length 20 ns. Stability of simulation is analyzed through root-mean-square deviation, beta factor (B-factor), and radius of gyration (Rg). Hydrogen bonds and their involvement in the structural stability of the enzyme are evaluated through radial distribution function. Newly developed application of axial frequency distribution that determines three-particle correlation on frequency distributions before and after simulation has provided a clear evidence for the movement of the inhibitor into active pocket of the enzyme. Results yielded strong interaction between enzyme and the inhibitor throughout the simulation. Binding of the inhibitor with enzyme has stabilized the enzyme structure; thus, the inhibitor has the potential to become a lead compound.
    Journal of biomolecular Structure & Dynamics 02/2015; DOI:10.1080/07391102.2014.1002423