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Develop and Test a Solvent Accessible Surface Area-Based Model in Conformational Entropy Calculations

Junmei Wang, Tingjun Hou
2012 Journal of Chemical Information and Modeling  
In this work, we have developed a fast approach to estimate the conformational entropy based upon solvent accessible surface area calculations.  ...  The weighted solvent accessible surface area (WSAS) model was extensively evaluated in three tests.  ...  Development of a Conformational Entropy Model Based on Weighted Solvent Accessible Surface Area In our algorithm, k in Eq. 4 is a tunable parameter.  ... 
doi:10.1021/ci300064d pmid:22497310 pmcid:PMC3360827 fatcat:nf2wwixhfjdkndgaxmc2ac6xkm

A GPU based Conformational Entropy Calculation Method

Qian Zhang, José M. García, Junmei Wang, Tingjun Hou, Horacio Emilio Pérez Sánchez
2013 International Work-Conference on Bioinformatics and Biomedical Engineering  
Here, instead of NMA, a solvent accessible surface area (SAS) based model was employed to compute the conformational entropy.  ...  Conformational entropy calculation, usually computed by normal mode analysis (NMA), is a time-consuming step in MM-PB/GBSA calculations.  ...  15290/PI/2010, by the Spanish MEC and European Commission FEDER under grants CSD2006-00046 and TIN2009-14475-C04.  ... 
dblp:conf/iwbbio/ZhangGWHS13 fatcat:5rf4jq5scnefbcobuq3buxo75m

An all atom energy based computational protocol for predicting binding affinities of protein-ligand complexes

Tarun Jain, B. Jayaram
2005 FEBS Letters  
The protocol builds in an all atom energy based empirical scoring function comprising electrostatics, van der Waals, hydrophobicity and loss of conformational entropy of protein side chains upon ligand  ...  Model validation and parameter analysis studies ensure the predictive ability of the scoring function.  ...  Pandey, Saher Afshan Sheikh and Praveen Aggarwal in preparing the manuscript and the web tool is acknowledged.  ... 
doi:10.1016/j.febslet.2005.10.031 pmid:16307743 fatcat:jjk5dyowonhx5jvlpt72xhroa4

Improved protein–ligand binding affinity prediction by using a curvature-dependent surface-area model

Yang Cao, Lei Li
2014 Bioinformatics  
Cyscore improves the prediction accuracy by using a novel curvature-dependent surface-area model, which is able to distinguish convex, planar and concave surface in hydrophobic free energy calculation.  ...  correlation and ranking tests.  ...  Zhi-Xiong Jim Xiao and Prof. Taijiao Jiang for the stimulating discussion, Prof. Jiang Zhu, Prof. Qintong Li and Dr Shuang Chen for critical review of the article.  ... 
doi:10.1093/bioinformatics/btu104 pmid:24563257 fatcat:tfdzaxrt2zhuriez2uuttvqv2y

Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces

Salim Bougouffa, Jim Warwicker
2008 BMC Bioinformatics  
Conclusion: We conclude that solvent accessible area, based on modelled mutant structures, is a poor correlate for ΔΔG upon mutation.  ...  A simple volume-based, rather than solvent accessibilitybased, model is constructed for ΔG and ΔΔG systems. This shows a more consistent behaviour.  ...  We thank Dr Nick Gresham for technical support, and James Kitchen, Tracey Bray and Pedro Chan for discussions.  ... 
doi:10.1186/1471-2105-9-448 pmid:18939984 pmcid:PMC2596146 fatcat:6rgo3ere7be3vn6avx4cut5zcy

The role of entropy and polarity in intermolecular contacts in protein crystals

Marcin Cieślik, Zygmunt S. Derewenda
2009 Acta Crystallographica Section D: Biological Crystallography  
It is shown that the propensity of a surface residue for incorporation into a crystal contact is not a linear function of its solvent-accessible surface area and that amino acids with low exposed surfaces  ...  , which are typically small and hydrophobic, have been underestimated with respect to their contact-forming potential by earlier area-based calculations.  ...  In principle, the discrepancy between the solvent-accessible surface and the contact-capable surface can be resolved in area-based calculations by the use of a more stringent lower ASA cutoff value of  ... 
doi:10.1107/s0907444909009500 pmid:19390155 pmcid:PMC2672819 fatcat:o4d6d462ynh6dohgxtbvzsyu44

An efficient method for analyzing conformational properties of a polymer in solvent

Ken-ich Amano, Hiraku Oshima, Masahiro Kinoshita
2011 Chemical Physics Letters  
We propose an efficient method for investigating conformational properties of a polymer in solvent.  ...  To illustrate it, we analyze conformations of a simple polymer chain stabilized in a hard-sphere solvent.  ...  Yoshidome for checking the results presented in Fig. 4 which can be done using the computer program for the morphometric approach developed by R. Roth, Y. Harano, and M. Kinoshita [4] .  ... 
doi:10.1016/j.cplett.2011.01.044 fatcat:jwv7rtlwebbb7mc2qj75ljrbr4

Binding energies of tyrosine kinase inhibitors: Error assessment of computational methods for imatinib and nilotinib binding

Clifford W. Fong
2015 Computational biology and chemistry  
A major error in inhibitorkinase binding lies in the non-polar solvation terms.  Solvent transfer free energies and the required empirical solvent accessible surface area factors for nilotinib and imatinib  ...  The QM based solvent model (PCM/SMD) gives different values from those used in the implicit PBSA solvent MM models.  ...  component and a non-polar component based on an arbitrary solvent accessible surface area (SASA) factor usually somewhere between 5-45 cal/mol/Å 2 .  ... 
doi:10.1016/j.compbiolchem.2015.05.002 pmid:26025598 fatcat:sn4sdm2pi5ddxkxsjxdt4sqkli

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

Samuel Genheden, Ulf Ryde
2015 Expert Opinion on Drug Discovery  
However, they contain several crude and questionable approximations, for example, the lack of conformational entropy and information about the number and free energy of water molecules in the binding site  ...  Areas covered: The authors review the use of MM/PBSA and MM/GBSA methods to calculate ligand-binding affinities, with an emphasis on calibration, testing and validation, as well as attempts to improve  ...  accessible surface area (SASA).  ... 
doi:10.1517/17460441.2015.1032936 pmid:25835573 pmcid:PMC4487606 fatcat:sa4y6inpyvcm3d35i7gjxziami

Thermodynamics of a reverse turn motif. Solvent effects and side-chain packing

Eugene Demchuk, Donald Bashford, Garry P. Gippert, David A. Case
1997 Journal of Molecular Biology  
The chain entropy of folding was calculated by a systematic search of accessible dihedral angle space.  ...  electrostatic model of polar solvation, and a surface areabased model of non-polar solvation.  ...  Acknowledgments We thank Dr Frank Eisenhaber for the program ASC, and P. E. Wright, J. Yao and H. J.  ... 
doi:10.1006/jmbi.1997.1103 pmid:9236131 fatcat:kdxzzloxjzejjknwjzvggpcm6m

On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions

Nicolas Froloff, Andreas Windemuth, Barry Honig
1997 Protein Science  
This paper describes a methodology to calculate the binding free energy (AG) of a protein-ligand complex using a continuum model of the solvent.  ...  degrees of freedom upon binding; A, solvent-accessible surface area; yaw, microscopic surface tension associated with the transfer of alkane from liquid alkane to water: E" dielectric constant of water  ...  N.F. was supported by a one-year LAVOISIER fellowship from the French Ministry of Foreign Affairs and by the I'Orkal company.  ... 
doi:10.1002/pro.5560060617 pmid:9194189 pmcid:PMC2143728 fatcat:zs7oujejyraivp7odhfcp6umku

Buried and Accessible Surface Area Control Intrinsic Protein Flexibility

Joseph A. Marsh
2013 Journal of Molecular Biology  
A simple proxy for this, the relative solvent accessible surface area (Arel), therefore shows excellent agreement with independent measures of global protein flexibility derived from various experimental  ...  Finally, local solvent accessibility is shown to be a primary determinant of local residue flexibility.  ...  Importance of solvent accessibility and contact surfaces in modeling side-chain conformations in proteins. J Comput Chem 25, 712-724 30.  ... 
doi:10.1016/j.jmb.2013.06.019 pmid:23811058 fatcat:lbmicbpzb5ho7pbnkvf7zjkv6e

Effect of Conformational Flexibility and Solvation on Receptor-Ligand Binding Free Energies

Sandor Vajda, Zhiping Wheng, Rakefet Rosenfeld, Charles DeLisi
1994 Biochemistry  
Flexibility introduces two additional terms in the free energy difference: the internal energy difference between the ligand in the bound and free states and the backbone entropy loss.  ...  The results are in good agreement with the measured values and somewhat better than those previously reported in the literature.  ...  Novotny for helpful discussions and for providing us with the programs implementing the binding free energy calculations described in Novotny et al. (1989) .  ... 
doi:10.1021/bi00251a004 pmid:7947806 fatcat:rjt572vhpnhppivjslyiuxz32e

Variational Optimization of an All-Atom Implicit Solvent Force Field To Match Explicit Solvent Simulation Data

Sandro Bottaro, Kresten Lindorff-Larsen, Robert B. Best
2013 Journal of Chemical Theory and Computation  
In order to achieve this, we have used a recently proposed coarse-graining procedure based on minimization of an entropy-related objective function to train the model to reproduce the equilibrium distribution  ...  Here, we present an efficient solvation term based on a Gaussian solvent-exclusion model (EEF1) for simulations of proteins in aqueous environment, with the primary aim of having a good overlap with explicit  ...  the solvent-accessible surface area.  ... 
doi:10.1021/ct400730n pmid:24748852 pmcid:PMC3987920 fatcat:4takx4g26jburmnnujjahxtisy

A novel method reveals that solvent water favors polyproline II over β-strand conformation in peptides and unfolded proteins: conditional hydrophobic accessible surface area (CHASA)

Patrick J. Fleming, Nicholas C. Fitzkee, Mihaly Mezei, Rajgopal Srinivasan, George D. Rose
2009 Protein Science  
This conditional hydrophobic accessible surface area is termed CHASA.  ...  It has been a long-standing goal to capture these solute-water energetics accurately and efficiently in calculations.  ...  Note added in proof CHASA software and a Web service to calculate CHASA-related parameters can be found at www.roselab.jhu.edu/chasa.  ... 
doi:10.1110/ps.041047005 pmid:15576559 pmcid:PMC2253334 fatcat:h4oe6pi2mvgtzj76azkxhzxnwi
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