Volume 26, Issue 5

Search all Journal of Computer-Aided Molecular Design articles

May 2012

Special Issue: SAMPL3: Blinded prediction of host-guest binding, hydration energies, and trypsin inhibition

Issue Editor:

A. Geoffrey Skillman

20 articles in this issue

SAMPL3: blinded prediction of host–guest binding affinities, hydration free energies, and trypsin inhibitors
A. Geoffrey Skillman
OriginalPaper 24 May 2012 Pages: 473 - 474
Blind prediction of host–guest binding affinities: a new SAMPL3 challenge
Hari S. Muddana
C. Daniel Varnado
Michael K. Gilson
OriginalPaper 25 February 2012 Pages: 475 - 487
The SAMPL3 blind prediction challenge: transfer energy overview
Matthew T. Geballe
J. Peter Guthrie
OriginalPaper 03 April 2012 Pages: 489 - 496
The DINGO dataset: a comprehensive set of data for the SAMPL challenge
Janet Newman
Olan Dolezal
Thomas S. Peat
OriginalPaper Open access 21 December 2011 Pages: 497 - 503
Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM)
Emilio Gallicchio
Ronald M. Levy
OriginalPaper 22 February 2012 Pages: 505 - 516
Prediction of SAMPL3 host–guest binding affinities: evaluating the accuracy of generalized force-fields
Hari S. Muddana
Michael K. Gilson
OriginalPaper 25 January 2012 Pages: 517 - 525
Binding affinities in the SAMPL3 trypsin and host–guest blind tests estimated with the MM/PBSA and LIE methods
Paulius Mikulskis
Samuel Genheden
Ulf Ryde
OriginalPaper 25 December 2011 Pages: 527 - 541
Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations
Gerhard König
Bernard R. Brooks
OriginalPaper 24 December 2011 Pages: 543 - 550
Alchemical prediction of hydration free energies for SAMPL
David L. Mobley
Shaui Liu
Julia E. Rice
Perspectives 24 December 2011 Pages: 551 - 562
Testing the semi-explicit assembly solvation model in the SAMPL3 community blind test
Charles W. Kehoe
Christopher J. Fennell
Ken A. Dill
OriginalPaper 29 December 2011 Pages: 563 - 568
Thermodynamic integration to predict host-guest binding affinities
Morgan Lawrenz
Jeff Wereszczynski
J. Andrew McCammon
OriginalPaper 16 February 2012 Pages: 569 - 576
Force-field and quantum-mechanical binding study of selected SAMPL3 host-guest complexes
Nobuko Hamaguchi
Laszlo Fusti-Molnar
Stanislaw Wlodek
OriginalPaper 25 February 2012 Pages: 577 - 582
A fragment-based approach to the SAMPL3 Challenge
John L. Kulp III
Seth N. Blumenthal
Frank Guarnieri
OriginalPaper 31 January 2012 Pages: 583 - 594
Evaluation of docking performance in a blinded virtual screening of fragment-like trypsin inhibitors
Georgiana Surpateanu
Bogdan I. Iorga
OriginalPaper 17 December 2011 Pages: 595 - 601
Computational fragment-based screening using RosettaLigand: the SAMPL3 challenge
Ashutosh Kumar
Kam Y. J. Zhang
OriginalPaper 15 January 2012 Pages: 603 - 616
Exhaustive search and solvated interaction energy (SIE) for virtual screening and affinity prediction
Traian Sulea
Hervé Hogues
Enrico O. Purisima
Perspectives 25 December 2011 Pages: 617 - 633
Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field
Oliver Beckstein
Bogdan I. Iorga
OriginalPaper 21 December 2011 Pages: 635 - 645
Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores
Mark L. Benson
John C. Faver
Kenneth M. Merz Jr.
OriginalPaper 04 April 2012 Pages: 647 - 659
Predicting hydration free energies of polychlorinated aromatic compounds from the SAMPL-3 data set with FiSH and LIE models
Traian Sulea
Enrico O. Purisima
OriginalPaper 22 December 2011 Pages: 661 - 667
Prediction of free energies of hydration with COSMO-RS on the SAMPL3 data set
Jens Reinisch
Andreas Klamt
Michael Diedenhofen
OriginalPaper 13 May 2012 Pages: 669 - 673

Volume 26, Issue 5

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