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There are 3488 results for: content related to: Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease

  1. Comparison of end-point continuum-solvation methods for the calculation of protein–ligand binding free energies

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 5, May 2012, Pages: 1326–1342, Samuel Genheden and Ulf Ryde

    Version of Record online : 13 FEB 2012, DOI: 10.1002/prot.24029

  2. Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI)

    Journal of Computational Chemistry

    Volume 36, Issue 25, September 30, 2015, Pages: 1859–1873, Pin-Chih Su, Cheng-Chieh Tsai, Shahila Mehboob, Kirk E. Hevener and Michael E. Johnson

    Version of Record online : 27 JUL 2015, DOI: 10.1002/jcc.24011

  3. Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

    Journal of Computational Chemistry

    Volume 32, Issue 5, 15 April 2011, Pages: 866–877, Tingjun Hou, Junmei Wang, Youyong Li and Wei Wang

    Version of Record online : 14 OCT 2010, DOI: 10.1002/jcc.21666

  4. Computational Investigation of SENP:SUMO Protein-Protein Interaction for Structure Based Drug Design

    Molecular Informatics

    Volume 32, Issue 3, March 2013, Pages: 267–280, Ashutosh Kumar and Kam Y. J. Zhang

    Version of Record online : 11 MAR 2013, DOI: 10.1002/minf.201200124

  5. Virtual screening using molecular simulations

    Proteins: Structure, Function, and Bioinformatics

    Volume 79, Issue 6, June 2011, Pages: 1940–1951, Tianyi Yang, Johnny C. Wu, Chunli Yan, Yuanfeng Wang, Ray Luo, Michael B. Gonzales, Kevin N. Dalby and Pengyu Ren

    Version of Record online : 12 APR 2011, DOI: 10.1002/prot.23018

  6. A challenging system: Free energy prediction for factor Xa

    Journal of Computational Chemistry

    Volume 32, Issue 8, June 2011, Pages: 1743–1752, Hannes G. Wallnoefer, Klaus R. Liedl and Thomas Fox

    Version of Record online : 4 MAR 2011, DOI: 10.1002/jcc.21758

  7. Predicting flexible loop regions that interact with ligands: The challenge of accurate scoring

    Proteins: Structure, Function, and Bioinformatics

    Volume 80, Issue 1, January 2012, Pages: 246–260, Matthew L. Danielson and Markus A. Lill

    Version of Record online : 9 NOV 2011, DOI: 10.1002/prot.23199

  8. Crystal molecular dynamics simulations to speed up MM/PB(GB)SA evaluation of binding free energies of di-mannose deoxy analogs with P51G-m4-Cyanovirin-N

    Journal of Computational Chemistry

    Volume 32, Issue 6, 30 April 2011, Pages: 1043–1053, Ivan I. Vorontsov and Osamu Miyashita

    Version of Record online : 14 OCT 2010, DOI: 10.1002/jcc.21683

  9. A semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections

    Journal of Computational Chemistry

    Volume 33, Issue 12, 5 May 2012, Pages: 1179–1189, Paulius Mikulskis, Samuel Genheden, Karin Wichmann and Ulf Ryde

    Version of Record online : 7 MAR 2012, DOI: 10.1002/jcc.22949

  10. How to obtain statistically converged MM/GBSA results

    Journal of Computational Chemistry

    Volume 31, Issue 4, March 2010, Pages: 837–846, Samuel Genheden and Ulf Ryde

    Version of Record online : 13 JUL 2009, DOI: 10.1002/jcc.21366

  11. You have free access to this content
    Application of MM/PBSA colony free energy to loop decoy discrimination: Toward correlation between energy and root mean square deviation

    Protein Science

    Volume 14, Issue 4, April 2005, Pages: 889–901, Federico Fogolari and Silvio C.E. Tosatto

    Version of Record online : 1 JAN 2009, DOI: 10.1110/ps.041004105

  12. Comparative Analysis of Various Electrostatic Potentials on Docking Precision Against Cyclin-Dependent Kinase 2 Protein: A Multiple Docking Approach

    Chemical Biology & Drug Design

    Volume 85, Issue 2, February 2015, Pages: 107–118, Sunil K. Tripathi, Rajendran Naga Soundarya, Poonam Singh and Sanjeev K. Singh

    Version of Record online : 12 JUL 2014, DOI: 10.1111/cbdd.12376

  13. Improvements, trends, and new ideas in molecular docking: 2012–2013 in review

    Journal of Molecular Recognition

    Volume 28, Issue 10, October 2015, Pages: 581–604, Elizabeth Yuriev, Jessica Holien and Paul A. Ramsland

    Version of Record online : 21 MAR 2015, DOI: 10.1002/jmr.2471

  14. Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA

    Journal of Computational Chemistry

    Volume 31, Issue 4, March 2010, Pages: 797–810, Giulio Rastelli, Alberto Del Rio, Gianluca Degliesposti and Miriam Sgobba

    Version of Record online : 30 JUN 2009, DOI: 10.1002/jcc.21372

  15. Molecular modeling reveals binding interface of γ-tubulin with GCP4 and interactions with noscapinoids

    Proteins: Structure, Function, and Bioinformatics

    Volume 83, Issue 5, May 2015, Pages: 827–843, Charu Suri, Harish C. Joshi and Pradeep Kumar Naik

    Version of Record online : 28 FEB 2015, DOI: 10.1002/prot.24773

  16. You have free access to this content
    Identification of New Peptide Ligands for Epidermal Growth Factor Receptor Using Phage Display and Computationally Modeling their Mode of Binding

    Chemical Biology & Drug Design

    Volume 79, Issue 3, March 2012, Pages: 246–259, Maryam Hamzeh-Mivehroud, Ali Mahmoudpour and Siavoush Dastmalchi

    Version of Record online : 11 JAN 2012, DOI: 10.1111/j.1747-0285.2011.01282.x

  17. Physics-based enzyme design: Predicting binding affinity and catalytic activity

    Proteins: Structure, Function, and Bioinformatics

    Volume 82, Issue 12, December 2014, Pages: 3397–3409, Sarah Sirin, David A. Pearlman and Woody Sherman

    Version of Record online : 30 OCT 2014, DOI: 10.1002/prot.24694

  18. Protein kinase C isozymes and their selectivity towards ruboxistaurin

    Proteins: Structure, Function, and Bioinformatics

    Volume 72, Issue 1, July 2008, Pages: 447–460, Sishi Tang, Victor Xiao, Lianhu Wei, Catharine I. Whiteside and Lakshmi P. Kotra

    Version of Record online : 23 JAN 2008, DOI: 10.1002/prot.21942

  19. Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein

    Biopolymers

    Volume 97, Issue 11, November 2012, Pages: 899–909, Zhili Zuo, Neha S. Gandhi, Katja M. Arndt and Ricardo L. Mancera

    Version of Record online : 13 AUG 2012, DOI: 10.1002/bip.22099

  20. FEW: A workflow tool for free energy calculations of ligand binding

    Journal of Computational Chemistry

    Volume 34, Issue 11, 30 April 2013, Pages: 965–973, Nadine Homeyer and Holger Gohlke

    Version of Record online : 3 JAN 2013, DOI: 10.1002/jcc.23218