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% Encoding: UTF-8
@Article{Dror2013,
author = {Dror, RO and Green, HF and Valant, C and Borhani, DW and Valcourt, JR and Pan, AC and Arlow, DH and Canals, M and Lane, JR and Rahmani, R and Baell, JB and Sexton, PM and Christopoulos, A and Shaw, DE},
title = {Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs},
journal = {Nature},
year = {2013},
volume = {503},
number = {7475},
pages = {295--299},
publisher = {Nature Publishing Group},
}
@Article{Treuel2013,
author = {Treuel, L and Brandholt, S and Maffre, P and Wiegele, S and Shang, L and Nienhaus, GU},
title = {Impact of Protein Modification on the Protein Corona on Nanoparticles and Nanoparticle-Cell Interactions},
journal = {ACS Nano},
year = {2013},
volume = {8},
number = {1},
pages = {503--513},
timestamp = {2017-06-25},
}
@Article{Northrup1984,
author = {Northrup, S.H. and Allison, S.A. and McCammon, J.A.},
title = {Brownian dynamics simulation of diffusion influenced bimolecular reactions},
journal = {Journal of Chemical Physics},
year = {1984},
volume = {80},
pages = {1517--1524},
publisher = {AIP Publishing},
}
@Article{Spiga2013a,
author = {Spiga, E and Alemani, D and Degiacomi, MT and Cascella, M and Peraro, MD},
title = {Brownian dynamics simulation of diffusion influenced bimolecular reactions},
journal = {Journal of Chemical Theory and Computation},
year = {2013},
volume = {9},
number = {8},
pages = {3515--3526},
timestamp = {2017-06-27},
}
@Article{Stansfeld2015,
author = {Stansfeld, Phillip J and Goose, Joseph E and Caffrey, M and Carpenter, Elisabeth P and Parker, Joanne L and Newstead, S and Sansom, Mark SP},
title = {MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes},
journal = {Structure},
year = {2015},
volume = {23},
number = {7},
pages = {1350--1361},
}
@Article{Song2004a,
author = {Song, Y and Zhang, Y and Bajaj, CL and Baker, NA},
title = {Continuum diffusion reaction rate calculations of wild-type and mutant mouse acetylcholinesterase: adaptive finite element analysis},
journal = {Biophysical Journal},
year = {2004},
volume = {87},
number = {3},
pages = {1558--1566},
}
@Article{Mereghetti2012,
author = {Mereghetti, P and Wade, RC},
title = {Atomic Detail {Brownian} Dynamics Simulations of Concentrated Protein Solutions with a Mean Field Treatment of Hydrodynamic Interactions},
journal = {Journal of Physical Chemistry},
year = {2012},
volume = {116},
number = {29},
pages = {8523--8533},
timestamp = {2017-06-27},
}
@Article{Decherchi2013,
author = {Decherchi, Sergio and Rocchia, Walter},
title = {A general and robust ray-casting-based algorithm for triangulating surfaces at the nanoscale},
journal = {PLoS ONE},
year = {2013},
volume = {8},
number = {4},
pages = {e59744},
publisher = {Public Library of Science},
}
@Article{Saad1986,
author = {Saad, Y. and Schultz, M.},
title = {{GMRES}: A generalized minimal residual algorithm for solving nonsymmetric linear systems},
journal = {Journal of Scientific and Statistical Computing},
year = {1986},
volume = {7},
pages = {856--869},
publisher = {SIAM},
timestamp = {2017-06-27},
}
@Article{Dolinsky2004,
author = {Dolinsky, Todd J and Nielsen, Jens E and McCammon, J Andrew and Baker, Nathan A},
title = {{PDB2PQR}: an automated pipeline for the setup of {Poisson--Boltzmann} electrostatics calculations},
journal = {Nucleic Acids Research},
year = {2004},
volume = {32},
number = {suppl 2},
pages = {W665--W667},
publisher = {Oxford Univ Press},
timestamp = {2017-06-27},
}
@Article{Ermak1978,
author = {Ermak, Donald and McCammon, J. A.},
title = {Brownian dynamics with hydrodynamic interactions},
journal = {Journal of Chemical Physics},
year = {1978},
volume = {69},
number = {4},
pages = {1352--1360},
publisher = {AIP Publishing},
}
@Article{Geng2013,
author = {Geng, Weihua and Krasny, Robert},
title = {A treecode-accelerated boundary integral {Poisson-Boltzmann} solver for electrostatics of solvated biomolecules},
journal = {Journal of Computational Physics},
year = {2013},
volume = {247},
pages = {62--78},
publisher = {Elsevier},
timestamp = {2017-06-27},
}
@Article{Li2009,
author = {Li, Peijun and Johnston, Hans and Krasny, Robert},
title = {A {Cartesian} treecode for screened {Coulomb} interactions},
journal = {Journal of Computational Physics},
year = {2009},
volume = {228},
pages = {3858--3868},
publisher = {Elsevier},
timestamp = {2017-06-27},
}
@Article{FEtk,
author = {Holst, Michael},
title = {Adaptive numerical treatment of elliptic systems on manifolds},
journal = {Journal of Computational Mathematics},
year = {2001},
volume = {15},
pages = {139--191},
timestamp = {2017-06-27},
}
@Book{Golub1996,
title = {Matrix Computations},
publisher = {Johns Hopkins University Press},
year = {1996},
author = {Golub, Gene H. and Van Loan, Charles F.},
address = {Baltimore, MD, USA},
edition = {3rd},
isbn = {0-8018-5414-8},
timestamp = {2017-06-22},
}
@Article{Purvine2016,
author = {Purvine, Emilie and Monson, Kyle and Jurrus, Elizabeth and Starr, Keith and Baker, Nathan A.},
title = {Energy Minimization of Discrete Protein Titration State Models Using Graph Theory},
journal = {Journal of Physical Chemistry},
year = {2016},
volume = {120},
pages = {8354--8360},
doi = {10.1021/acs.jpcb.6b02059},
publisher = {ACS Publications},
}
@Article{Herraez2006,
author = {Herraez, Angel},
title = {Biomolecules in the computer: {Jmol} to the rescue},
journal = {Biochemistry and Molecular Biology Education},
year = {2006},
volume = {34},
number = {4},
pages = {255--261},
publisher = {Wiley Online Library},
timestamp = {2017-06-27},
}
@Article{Jones2005,
author = {Jones, Loretta L and Jordan, Kenneth D and Stillings, Neil A},
title = {Molecular visualization in chemistry education: the role of multidisciplinary collaboration},
journal = {Chemistry Education Research and Practice},
year = {2005},
volume = {6},
number = {3},
pages = {136--149},
publisher = {Royal Society of Chemistry},
}
@Article{Juffer1991,
author = {Juffer, Andr\'{e} and Botta, Eugen and van Keulen, Bert and van der Ploeg, Auke and Berendsen, Herman},
title = {The electric potential of a macromolecule in a solvent: A fundamental approach},
journal = {Journal of Computational Physics},
year = {1991},
volume = {97},
number = {1},
pages = {144--171},
publisher = {Elsevier},
timestamp = {2017-06-27},
}
@Article{Sarkar2012,
author = {Li, L and Li, C and Sarkar, S and Zhang, J and Witham, S and Zhang, Z and Wang, L and Smith, N and Petukh, M and Alexov, E},
title = {DelPhi: a comprehensive suite for DelPhi software and associated resources},
journal = {BMC Biophysics},
year = {2012},
volume = {5},
pages = {9},
doi = {10.1186/2046-1682-5-9},
timestamp = {2017-08-11},
}
@InProceedings{Krishnan2009,
author = {Krishnan, Sriram and Clementi, Luca and Ren, Jingyuan and Papadopoulos, Philip and Li, Wilfred},
title = {Design and evaluation of {Opal2}: A toolkit for scientific software as a service},
booktitle = {Services-I, 2009 World Conference on},
year = {2009},
pages = {709--716},
organization = {IEEE},
timestamp = {2017-06-27},
url = {http://nbcr-222.ucsd.edu/opal2/dashboard},
}
@Article{Bochevarov2013,
author = {Bochevarov, AD and Harder, E and Hughes, TF and Greenwood, JR and Braden, DA and Philipp, DM and Rinaldo, D and Halls, MD and Zhang, J and Friesner, RA},
title = {Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences},
journal = {International Journal of Quantum Chemistry},
year = {2013},
volume = {113},
number = {18},
pages = {2110--2142},
timestamp = {2017-06-27},
}
@Article{Grant2001,
author = {Grant, JA and Pickup, BT and Nicholls, A},
title = {A smooth permittivity function for {Poisson-Boltzmann} solvation methods},
journal = {Journal of Computational Chemistry},
year = {2001},
volume = {22},
pages = {608--640},
publisher = {Wiley},
timestamp = {2017-06-27},
}
@Article{Chen2011a,
author = {Chen, D and Chen, Z and Chen, C and Geng, W and Wei, GW},
title = {MIBPB: A software package for electrostatic analysis},
journal = {Journal of Computational Chemistry},
year = {2011},
volume = {32},
number = {4},
pages = {756--770},
publisher = {Wiley},
timestamp = {2017-06-27},
}
@InProceedings{Evangelidis2009,
author = {Evangelidis, T. and Bourne, P.E. and Xie, L. and Xie, L.},
title = {An integrated workflow for proteome-wide off-target identification and polypharmacology drug design},
booktitle = {International Conference on Bioinformatics and Biomedicine Workshops},
year = {2009},
pages = {32--39},
organization = {IEEE},
url = {doi: 10.1109/BIBMW.2012.6470348},
}
@Article{Lotan2006,
author = {Lotan, Itay and Head-Gordon, Teresa},
title = {An Analytical Electrostatic Model for Salt Screened Interactions between Multiple Proteins},
journal = {Journal of Chemical Theory and Computation},
year = {2006},
volume = {2},
number = {3},
pages = {541--555},
note = {PMID: 26626662},
doi = {10.1021/ct050263p},
eprint = {http://dx.doi.org/10.1021/ct050263p},
timestamp = {2017-06-27},
}
@Article{Yap2013,
author = {Yap, E. H. and Head-Gordon, T.},
title = {Calculating the Bimolecular Rate of Protein-Protein Association with Interacting Crowders},
journal = {Journal of Chemical Theory and Computation},
year = {2013},
volume = {9},
number = {5},
pages = {2481--9},
issn = {1549-9618 (Print) 1549-9618 (Linking)},
doi = {10.1021/ct400048q},
timestamp = {2017-06-27},
type = {Journal Article},
url = {http://www.ncbi.nlm.nih.gov/pubmed/26583736},
}
@Article{Rego2015,
author = {Rego, Nicholas and Koes, David},
title = {{3Dmol.js}: molecular visualization with {WebGL}},
journal = {Bioinformatics},
year = {2015},
volume = {31},
number = {8},
pages = {1322--1324},
publisher = {Oxford Univ Press},
timestamp = {2017-06-27},
url = {http://3dmol.csb.pitt.edu/},
}
@InProceedings{Sanner1995,
author = {Sanner, Michel and Olson, Arthur and Spehner, Jean Claude},
title = {Fast and robust computation of molecular surfaces},
booktitle = {Proc 11th ACM Symp Comp Geom},
year = {1995},
pages = {C6-C7},
organization = {ACM},
}
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author = {Barnes, Josh and Hut, Piet},
title = {A hierarchical $\mathcal{O}(N \log N)$ force-calculation algorithm},
journal = {Nature},
year = {1986},
volume = {324},
pages = {446--449},
publisher = {Nature Publishing Group},
timestamp = {2017-06-22},
}
@Article{Li2005,
author = {Li, H. and Robertson, A. D. and Jensen, J. H.},
title = {Very fast empirical prediction and rationalization of protein {p$K_a$} values},
journal = {Proteins},
year = {2005},
volume = {61},
pages = {704721},
publisher = {Wiley},
timestamp = {2017-06-27},
}
@Article{Sondergaard2011,
author = {Sondergaard, Chresten R. and Olsson, Mats HM and Rostkowski, Michal and Jensen, Jan H.},
title = {Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of {p$K_a$} Values},
journal = {Journal of Chemical Theory and Computation},
year = {2011},
volume = {7},
number = {7},
pages = {2284--2295},
timestamp = {2017-06-27},
type = {Journal Article},
}
@Article{Mobley2014,
author = {Mobley, D L and Wymer, K L and Lim, N M and Guthrie, J P},
title = {Blind prediction of solvation free energies from the {SAMPL4} challenge},
journal = {Journal of Computer-Aided Molecular Design},
year = {2014},
volume = {28},
number = {3},
pages = {135--50},
abstract = {Here, we give an overview of the small molecule hydration portion of the SAMPL4 challenge, which focused on predicting hydration free energies for a series of 47 small molecules. These gas-to-water transfer free energies have in the past proven a valuable test of a variety of computational methods and force fields. Here, in contrast to some previous SAMPL challenges, we find a relatively wide range of methods perform quite well on this test set, with RMS errors in the 1.2 kcal/mol range for several of the best performing methods. Top-performers included a quantum mechanical approach with continuum solvent models and functional group corrections, alchemical molecular dynamics simulations with a classical all-atom force field, and a single-conformation Poisson-Boltzmann approach. While 1.2 kcal/mol is still a significant error, experimental hydration free energies covered a range of nearly 20 kcal/mol, so methods typically showed substantial predictive power. Here, a substantial new focus was on evaluation of error estimates, as predicting when a computational prediction is reliable versus unreliable has considerable practical value. We found, however, that in many cases errors are substantially underestimated, and that typically little effort has been invested in estimating likely error. We believe this is an important area for further research.},
bdsk-url-1 = {http://dx.doi.org/10.1007/s10822-014-9718-2},
date-added = {2016-05-12 23:52:17 +0000},
date-modified = {2016-05-12 23:52:42 +0000},
doi = {10.1007/s10822-014-9718-2},
journal-full = {Journal of computer-aided molecular design},
mesh = {Computer Simulation; Models, Chemical; Small Molecule Libraries; Thermodynamics; Water},
owner = {to-file},
pmc = {PMC4006301},
pmid = {24615156},
pst = {ppublish},
timestamp = {2017-06-27},
}
@Article{Sansone2008,
author = {Sansone, S-A and Rocca-Serra, P and Brandizi, M and Brazma, A and Field, D and Fostel, J and Garrow, A G and Gilbert, J and Goodsaid, F and Hardy, N and Jones, P and Lister, A and Miller, M and Morrison, N and Rayner, T and Sklyar, N and Taylor, C and Tong, W and Warner, G and Wiemann, S and {Members of the RSBI Working Group}},
title = {The first {RSBI (ISA-TAB)} workshop: "can a simple format work for complex studies?"},
journal = {OMICS},
year = {2008},
volume = {12},
number = {2},
pages = {143--9},
abstract = {This article summarizes the motivation for, and the proceedings of, the first ISA-TAB workshop held December 6-8, 2007, at the EBI, Cambridge, UK. This exploratory workshop, organized by members of the Microarray Gene Expression Data (MGED) Society's Reporting Structure for Biological Investigations (RSBI) working group, brought together a group of developers of a range of collaborative systems to discuss the use of a common format to address the pressing need of reporting and communicating data and metadata from biological, biomedical, and environmental studies employing combinations of genomics, transcriptomics, proteomics, and metabolomics technologies along with more conventional methodologies. The expertise of the participants comprised database development, data management, and hands-on experience in the development of data communication standards. The workshop's outcomes are set to help formalize the proposed Investigation, Study, Assay (ISA)-TAB tab-delimited format for representing and communicating experimental metadata. This article is part of the special issue of OMICS on the activities of the Genomics Standards Consortium (GSC).},
bdsk-url-1 = {http://dx.doi.org/10.1089/omi.2008.0019},
date-added = {2016-05-12 23:50:21 +0000},
date-modified = {2016-05-12 23:51:28 +0000},
doi = {10.1089/omi.2008.0019},
journal-full = {Omics : a journal of integrative biology},
mesh = {Computational Biology; Database Management Systems; Education; Genomics; Great Britain; Proteomics; RNA, Messenger},
owner = {to-file},
pmid = {18447634},
pst = {ppublish},
timestamp = {2017-06-22},
}
@Article{Morin2013,
author = {Morin, A and Eisenbraun, B and Key, J and Sanschagrin, P C and Timony, M A and Ottaviano, M and Sliz, P},
title = {Collaboration gets the most out of software},
journal = {Elife},
year = {2013},
volume = {2},
pages = {e01456},
abstract = {By centralizing many of the tasks associated with the upkeep of scientific software, SBGrid allows researchers to spend more of their time on research.},
bdsk-url-1 = {http://dx.doi.org/10.7554/eLife.01456},
date-added = {2016-05-12 23:48:45 +0000},
date-modified = {2016-05-12 23:49:09 +0000},
doi = {10.7554/eLife.01456},
journal-full = {eLife},
keywords = {Cutting edge; computational tools and techniques; research computing; software},
mesh = {Computational Biology; Cooperative Behavior; Humans; Information Dissemination; Software},
owner = {to-file},
pmc = {PMC3771563},
pmid = {24040512},
pst = {epublish},
timestamp = {2017-06-22},
}
@Article{Kieseritzky2008,
author = {Kieseritzky, G and Knapp, E-W},
title = {Optimizing {p$K_a$} computation in proteins with {pH} adapted conformations},
journal = {Proteins},
year = {2008},
volume = {71},
number = {3},
pages = {1335--48},
abstract = {pK(A) in proteins are determined by electrostatic energy computations using a small number of optimized protein conformations derived from crystal structures. In these protein conformations hydrogen positions and geometries of salt bridges on the protein surface were determined self-consistently with the protonation pattern at three pHs (low, ambient, and high). Considering salt bridges at protein surfaces is most relevant, since they open at low and high pH. In the absence of these conformational changes, computed pK(A)(comp) of acidic (basic) groups in salt bridges underestimate (overestimate) experimental pK(A)(exp), dramatically. The pK(A)(comp) for 15 different proteins with 185 known pK(A)(exp) yield an RMSD of 1.12, comparable with two other methods. One of these methods is fully empirical with many adjustable parameters. The other is also based on electrostatic energy computations using many non-optimized side chain conformers but employs larger dielectric constants at short distances of charge pairs that diminish their electrostatic interactions. These empirical corrections that account implicitly for additional conformational flexibility were needed to describe the energetics of salt bridges appropriately. This is not needed in the present approach. The RMSD of the present approach improves if one considers only strongly shifted pK(A)(exp) in contrast to the other methods under these conditions. Our method allows interpreting pK(A)(comp) in terms of pH dependent hydrogen bonding pattern and salt bridge geometries. A web service is provided to perform pK(A) computations.},
bdsk-url-1 = {http://dx.doi.org/10.1002/prot.21820},
date-added = {2016-05-12 23:47:16 +0000},
date-modified = {2016-05-12 23:47:52 +0000},
doi = {10.1002/prot.21820},
journal-full = {Proteins},
mesh = {Computational Biology; Hydrogen-Ion Concentration; Protein Conformation; Proteins; Static Electricity; Thermodynamics},
owner = {to-file},
pmid = {18058906},
pst = {ppublish},
timestamp = {2017-06-22},
}
@Article{Pettersen2004,
author = {Pettersen, E F and Goddard, T D and Huang, C C and Couch, G S and Greenblatt, D M and Meng, E C and Ferrin, T E},
title = {{UCSF Chimera}--a visualization system for exploratory research and analysis},
journal = {Journal of Computational Chemistry},
year = {2004},
volume = {25},
number = {13},
pages = {1605--12},
abstract = {The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.},
bdsk-url-1 = {http://dx.doi.org/10.1002/jcc.20084},
date-added = {2016-05-12 23:15:06 +0000},
date-modified = {2016-05-12 23:15:25 +0000},
doi = {10.1002/jcc.20084},
journal-full = {Journal of computational chemistry},
mesh = {Amino Acid Sequence; Computer Graphics; Models, Molecular; Molecular Conformation; Molecular Sequence Data; Research; Sequence Alignment; Software; Thermodynamics},
owner = {to-file},
pmid = {15264254},
pst = {ppublish},
timestamp = {2017-06-27},
}
@Unpublished{3Dmolweb,
author = {Koes, D},
title = {{3Dmol.js}},
note = {\url{http://3dmol.csb.pitt.edu/}},
date-added = {2016-05-12 23:06:25 +0000},
date-modified = {2016-05-12 23:06:47 +0000},
owner = {to-file},
timestamp = {2017-06-27},
url = {http://3dmol.csb.pitt.edu/},
urldate = {2016},
}
@Article{Hanson2010,
author = {Hanson, R M},
title = {{Jmol} - a paradigm shift in crystallographic visualization},
journal = {Journal of Applied Crystallography},
year = {2010},
volume = {43},
pages = {1250--1260},
issn = {0021-8898},
abstract = {Recent advances in molecular and crystallographic visualization methods are allowing instructors unprecedented opportunities to enhance student learning using virtual models within a familiar web-browser context. In step with these advances, the latest versions of the Jmol molecular visualization applet offer capabilities that hold potential for revolutionizing the way students learn about symmetry, uncertainty and the overall enterprise of molecular structure determination.},
address = {COMMERCE PLACE, 350 MAIN ST, MALDEN 02148, MA USA},
}
@Article{Page2006,
author = {Page, C S and Bates, P A},
title = {Can {MM-PBSA} calculations predict the specificities of protein kinase inhibitors?},
journal = {Journal of Computational Chemistry},
year = {2006},
volume = {27},
number = {16},
pages = {1990--2007},
abstract = {An application of the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) protocol to the prediction of protein kinase inhibitor selectivity is presented. Six different inhibitors are placed in equivalent orientations in each of six different receptors. Fully solvated molecular dynamics is then run for 1 ns on each of the 36 complexes, and the resulting trajectories scored, using the implicit solvent model. The results show some correlation with experimentally-determined specificities; anomalies may be attributed to a variety of causes, including difficulties in quantifying induced fit penalties and variabilities in normal modes calculations. Decomposing interaction energies on a per-residue basis yields more useful insights into the natures of the binding modes and suggests that the real value of such calculations lies in understanding interactions rather than outright prediction.},
bdsk-url-1 = {http://dx.doi.org/10.1002/jcc.20534},
date-added = {2016-05-12 22:54:42 +0000},
date-modified = {2016-05-12 22:55:00 +0000},
doi = {10.1002/jcc.20534},
journal-full = {Journal of computational chemistry},
mesh = {Amino Acid Sequence; Binding Sites; Computer Simulation; Ligands; Models, Chemical; Models, Molecular; Molecular Sequence Data; Protein Conformation; Protein Kinase Inhibitors; Protein Kinases; Protein Structure, Secondary; Sequence Alignment; Stereoisomerism; Structure-Activity Relationship; Substrate Specificity},
owner = {to-file},
pmid = {17036304},
pst = {ppublish},
timestamp = {2017-06-22},
}
@Article{Grazioso2008,
author = {Grazioso, G and Cavalli, A and De Amici, M and Recanatini, MauriMzio and De Micheli, C},
title = {$\alpha$7 nicotinic acetylcholine receptor agonists: prediction of their binding affinity through a molecular mechanics {Poisson-Boltzmann} surface area approach},
journal = {Journal of Computational Chemistry},
year = {2008},
volume = {29},
number = {15},
pages = {2593--602},
abstract = {A group of agonists for the alpha7 neuronal nicotinic acetylcholine receptors (nAChRs) was investigated, and their free energies of binding DeltaG(bind) were calculated by applying the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach. This method, based on molecular dynamics simulations of fully solvated protein-ligand complexes, allowed us to estimate the contribution of both polar and nonpolar terms as well as the entropy to the overall free energy of binding. The calculated results were in a good agreement with the experimentally determined DeltaG(bind) values, thereby pointing to the MM-PBSA protocol as a valuable computational tool for the rational design of specific agents targeting the neuronal alpha7 nAChR subtypes.},
bdsk-url-1 = {http://dx.doi.org/10.1002/jcc.21019},
date-added = {2016-05-12 22:52:55 +0000},
date-modified = {2016-05-12 22:53:22 +0000},
doi = {10.1002/jcc.21019},
journal-full = {Journal of computational chemistry},
mesh = {Computer Simulation; Humans; Models, Chemical; Nicotinic Agonists; Receptors, Nicotinic; Thermodynamics; alpha7 Nicotinic Acetylcholine Receptor},
owner = {to-file},
pmid = {18478580},
pst = {ppublish},
timestamp = {2017-06-22},
}
@Article{Islam2016,
author = {Islam, B and Stadlbauer, P and Neidle, S and Haider, S and Sponer, J},
title = {Can We Execute Reliable {MM-PBSA} Free Energy Computations of Relative Stabilities of Different Guanine Quadruplex Folds?},
journal = {Journal of Physical Chemistry B},
year = {2016},
volume = {120},
number = {11},
pages = {2899--912},
abstract = {The self-assembly and stability of DNA G-quadruplexes (GQs) are affected by the intrinsic stability of different GpG base steps embedded in their G-quartet stems. We have carried out MD simulations followed by MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) free energy calculations on all the experimentally observed three-quartet intramolecular human telomeric GQ topologies. We also studied antiparallel GQ models with alternative syn-anti patterns of the G-quartets. We tested different ions, dihedral variants of the DNA force field, water models, and simulation lengths. In total, ~35 �s of simulations have been carried out. The systems studied here are considerably more complete than the previously analyzed two-quartet stems. Among other effects, our computations included the stem-loop coupling and ion-ion interactions inside the stem. The calculations showed a broad agreement with the earlier predictions. However, the increase in the completeness of the system was associated with increased noise of the free energy data which could be related, for example, to the presence of long-lived loop substates and rather complex dynamics for the two bound ions inside the G-stem. As a result, the MM-PBSA data were noisy and we could not improve their quantitative convergence even by expanding the simulations to 2.5 �s long trajectories. We also suggest that the quality of MM-based free energy computations based on MD simulations of complete GQs is more sensitive to the neglect of explicit polarization effects, which, in real systems, are associated with the presence of multiple closely spaced ions inside the GQs. Thus, although the MM-PBSA procedure provides very useful insights that complement the structural-dynamics data from MD trajectories of GQs, the method is far from reaching quantitative accuracy. Our conclusions are in agreement with critical assessments of the MM-PBSA methodology available in contemporary literature for other types of problems.},
bdsk-url-1 = {http://dx.doi.org/10.1021/acs.jpcb.6b01059},
date-added = {2016-05-12 22:51:06 +0000},
date-modified = {2016-05-12 22:51:30 +0000},
doi = {10.1021/acs.jpcb.6b01059},
journal-full = {The journal of physical chemistry. B},
owner = {to-file},
pmid = {26918369},
pst = {ppublish},
timestamp = {2017-06-22},
}
@Article{Kumari2014,
author = {Kumari, R and Kumar, R and {Open Source Drug Discovery Consortium} and Lynn, A},
title = {{g\_mmpbsa} -- a {GROMACS} tool for high-throughput {MM-PBSA} calculations},
journal = {Journal of Chemical Information and Modeling},
year = {2014},
volume = {54},
number = {7},
pages = {1951--62},
abstract = {Molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), a method to estimate interaction free energies, has been increasingly used in the study of biomolecular interactions. Recently, this method has also been applied as a scoring function in computational drug design. Here a new tool g\_mmpbsa, which implements the MM-PBSA approach using subroutines written in-house or sourced from the GROMACS and APBS packages is described. g\_mmpbsa was developed as part of the Open Source Drug Discovery (OSDD) consortium. Its aim is to integrate high-throughput molecular dynamics (MD) simulations with binding energy calculations. The tool provides options to select alternative atomic radii and different nonpolar solvation models including models based on the solvent accessible surface area (SASA), solvent accessible volume (SAV), and a model which contains both repulsive (SASA-SAV) and attractive components (described using a Weeks-Chandler-Andersen like integral method). We showcase the effectiveness of the tool by comparing the calculated interaction energy of 37 structurally diverse HIV-1 protease inhibitor complexes with their experimental binding free energies. The effect of varying several combinations of input parameters such as atomic radii, dielectric constant, grid resolution, solute-solvent dielectric boundary definition, and nonpolar models was investigated. g\_mmpbsa can also be used to estimate the energy contribution per residue to the binding energy. It has been used to identify those residues in HIV-1 protease that are most critical for binding a range of inhibitors.},
bdsk-url-1 = {http://dx.doi.org/10.1021/ci500020m},
date-added = {2016-05-12 22:47:41 +0000},
date-modified = {2016-05-12 22:56:05 +0000},
doi = {10.1021/ci500020m},
journal-full = {Journal of chemical information and modeling},
mesh = {Drug Discovery; HIV Protease; HIV Protease Inhibitors; Molecular Dynamics Simulation; Solvents; Thermodynamics},
owner = {to-file},
pmid = {24850022},
pst = {ppublish},
timestamp = {2017-06-27},
}
@Article{Pabit2016,
author = {Pabit, S A and Katz, A M and Tolokh, I S and Drozdetski, A and Baker, N and Onufriev, A V and Pollack, L},
title = {Understanding Nucleic Acid Structural Changes by Comparing Wide-Angle X-ray Scattering {(WAXS)} Experiments to Molecular Dynamics Simulations},
journal = {Journal of Chemical Physics},
year = {2016},
volume = {144},
number = {20},
pages = {10106314950814},
abstract = {Wide-angle x-ray scattering (WAXS) is emerging as a powerful tool for increasing the resolution of solution structure measurements of biomolecules. Compared to its better known complement, small angle x-ray scattering (SAXS), WAXS targets higher scattering angles and can enhance structural studies of molecules by accessing finer details of solution structures. Although the extension from SAXS to WAXS is easy to implement experimentally, the computational tools required to fully harness the power of WAXS are still under development. Currently, WAXS is employed to study structural changes and ligand binding in proteins; however, the methods are not as fully developed for nucleic acids. Here, we show how WAXS can qualitatively characterize nucleic acid structures as well as the small but significant structural changes driven by the addition of multivalent ions. We show the potential of WAXS to test all-atom molecular dynamics (MD) simulations and to provide insight into understanding how the trivalent ion cobalt(III) hexammine (CoHex) affects the structure of RNA and DNA helices. We find that MD simulations capture the RNA structural change that occurs due to addition of CoHex.},
date-added = {2016-05-12 13:57:18 +0000},
date-modified = {2016-05-12 13:58:41 +0000},
doi = {10.1063/1.4950814},
owner = {to-file},
timestamp = {2017-06-22},
}
@Article{Sharp1991,
author = {Sharp, K A and Nicholls, A and Fine, R F and Honig, B},
title = {Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects},
journal = {Science},
year = {1991},
volume = {252},
number = {5002},
pages = {106--9},
abstract = {The magnitude of the hydrophobic effect, as measured from the surface area dependence of the solubilities of hydrocarbons in water, is generally thought to be about 25 calories per mole per square angstrom (cal mol-1 A-2). However, the surface tension at a hydrocarbon-water interface, which is a "macroscopic" measure of the hydrophobic effect, is approximately 72 cal mol-1 A-2. In an attempt to reconcile these values, alkane solubility data have been reevaluated to account for solute-solvent size differences, leading to a revised "microscopic" hydrophobic effect of 47 cal mol-1 A-2. This value, when used in a simple geometric model for the curvature dependence of the hydrophobic effect, predicts a macroscopic alkane-water surface tension that is close to the macroscopic value.},
date-added = {2016-05-12 13:49:23 +0000},
date-modified = {2016-05-12 13:49:23 +0000},
journal-full = {Science (New York, N.Y.)},
mesh = {Hydrocarbons; Solubility; Thermodynamics; Water},
owner = {to-file},
pmid = {2011744},
pst = {ppublish},
timestamp = {2017-06-22},
}
@Article{Swanson2005,
author = {Swanson, J M J and Mongan, J and McCammon, J A},
title = {Limitations of atom-centered dielectric functions in implicit solvent models},
journal = {Journal of Physical Chemistry B},
year = {2005},
volume = {109},
number = {31},
pages = {14769--72},
abstract = {Many recent advances in Poisson-Boltzmann and generalized Born implicit solvent models have used atom-centered polynomial or Gaussian functions to define the boundary separating low and high dielectric regions. In contrast to the Lee and Richards molecular surface, atom-centered surfaces result in interatomic crevices and buried pockets of high dielectric which are too small for a solvent molecule to occupy. We show that these interstitial high dielectric regions are of significant magnitude in globular proteins, that they artificially increase solvation energies, and that they distort the free energy surface of nonbonded interactions. These results suggest that implicit solvent dielectric functions must exclude interstitial high dielectric regions in order to yield physically meaningful results.},
bdsk-url-1 = {http://dx.doi.org/10.1021/jp052883s},
date-added = {2016-05-12 13:45:30 +0000},
date-modified = {2016-05-12 13:45:47 +0000},
doi = {10.1021/jp052883s},
journal-full = {The journal of physical chemistry. B},
mesh = {Electrons; Histidine; Models, Chemical; Solutions; Solvents; Static Electricity},
owner = {to-file},
pmid = {16852866},
pst = {ppublish},
timestamp = {2017-06-22},
}
@Article{Dong2003,
author = {Dong, Feng and Vijayakumar, M and Zhou, Huan-Xiang},
title = {Comparison of calculation and experiment implicates significant electrostatic contributions to the binding stability of barnase and barstar},
journal = {Biophysical Journal},
year = {2003},
volume = {85},
number = {1},
pages = {49--60},
abstract = {The contributions of electrostatic interactions to the binding stability of barnase and barstar were studied by the Poisson-Boltzmann model with three different protocols: a), the dielectric boundary specified as the van der Waals (vdW) surface of the protein along with a protein dielectric constant (epsilon (p)) of 4; b), the dielectric boundary specified as the molecular (i.e., solvent-exclusion (SE)) surface along with epsilon (p) = 4; and c), "SE + epsilon (p) = 20." The "vdW + epsilon (p) = 4" and "SE + epsilon (p) = 20" protocols predicted an overall electrostatic stabilization whereas the "SE + epsilon (p) = 4" protocol predicted an overall electrostatic destabilization. The "vdW + epsilon (p) = 4" protocol was most consistent with experiment. It quantitatively reproduced the observed effects of 17 mutations neutralizing charged residues lining the binding interface and the measured coupling energies of six charge pairs across the interface and reasonably rationalized the experimental ionic strength and pH dependences of the binding constant. In contrast, the "SE + epsilon (p) = 4" protocol predicted significantly larger coupling energies of charge pairs whereas the "SE + epsilon (p) = 20" protocol did not predict any pH dependence. This study calls for further scrutiny of the different Poisson-Boltzmann protocols and demonstrates potential danger in drawing conclusions on electrostatic contributions based on a particular calculation protocol.},
bdsk-url-1 = {http://dx.doi.org/10.1016/S0006-3495(03)74453-1},
date-added = {2016-05-12 13:42:07 +0000},
date-modified = {2016-05-12 13:42:07 +0000},
doi = {10.1016/S0006-3495(03)74453-1},
journal-full = {Biophysical journal},
mesh = {Bacterial Proteins; Binding Sites; Computer Simulation; Electrochemistry; Energy Transfer; Enzyme Activation; Enzyme Stability; Hydrogen-Ion Concentration; Kinetics; Macromolecular Substances; Models, Chemical; Models, Molecular; Protein Binding; Protein Conformation; Protein Subunits; Proteins; Ribonucleases; Static Electricity; Substrate Specificity},
owner = {to-file},
pmc = {PMC1303064},
pmid = {12829463},
pst = {ppublish},
timestamp = {2017-06-22},
}
@Article{Martinez2015,
author = {Martinez, Michael and Bruce, Neil J and Romanowska, Julia and Kokh, Daria B and Ozboyaci, Musa and Yu, Xiaofeng and {\"O}zt{\"u}rk, Mehmet Ali and Richter, Stefan and Wade, Rebecca C},
title = {{SDA 7}: A modular and parallel implementation of the simulation of diffusional association software},
journal = {Journal of Computational Chemistry},
year = {2015},
volume = {36},
number = {21},
pages = {1631--45},
abstract = {The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein-protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to simulate the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration-dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the parallelization of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object-oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the parallel performance.},
bdsk-url-1 = {http://dx.doi.org/10.1002/jcc.23971},
date-added = {2016-05-12 13:36:03 +0000},
date-modified = {2016-05-12 13:36:03 +0000},
doi = {10.1002/jcc.23971},
journal-full = {Journal of computational chemistry},
keywords = {Brownian dynamics; biomacromolecular diffusion; macromolecular association; parallelization; protein adsorption; protein flexibility; protein-solid state interactions},
mesh = {Algorithms; Bacillus; Computer Simulation; Diffusion; Models, Chemical; Models, Molecular; Proteins; Ribonucleases; Software},
owner = {to-file},
pmc = {PMC4755232},
pmid = {26123630},
pst = {ppublish},
timestamp = {2017-06-27},
}
@Article{Richter2008,
author = {Richter, S and Wenzel, A and Stein, M and Gabdoulline, R R and Wade, R C},
title = {{webPIPSA}: a web server for the comparison of protein interaction properties},
journal = {Nucleic Acids Res},
year = {2008},
volume = {36},
number = {Web Server issue},
pages = {W276-80},
abstract = {Protein molecular interaction fields are key determinants of protein functionality. PIPSA (Protein Interaction Property Similarity Analysis) is a procedure to compare and analyze protein molecular interaction fields, such as the electrostatic potential. PIPSA may assist in protein functional assignment, classification of proteins, the comparison of binding properties and the estimation of enzyme kinetic parameters. webPIPSA is a web server that enables the use of PIPSA to compare and analyze protein electrostatic potentials. While PIPSA can be run with downloadable software (see http://projects.eml.org/mcm/software/pipsa), webPIPSA extends and simplifies a PIPSA run. This allows non-expert users to perform PIPSA for their protein datasets. With input protein coordinates, the superposition of protein structures, as well as the computation and analysis of electrostatic potentials, is automated. The results are provided as electrostatic similarity matrices from an all-pairwise comparison of the proteins which can be subjected to clustering and visualized as epograms (tree-like diagrams showing electrostatic potential differences) or heat maps. webPIPSA is freely available at: http://pipsa.eml.org.},
bdsk-url-1 = {http://dx.doi.org/10.1093/nar/gkn181},
date-added = {2016-05-12 13:34:02 +0000},
date-modified = {2016-05-12 13:34:41 +0000},
doi = {10.1093/nar/gkn181},
journal-full = {Nucleic acids research},
mesh = {Enzymes; Internet; Protein Interaction Mapping; Proteins; Software; Static Electricity; Triose-Phosphate Isomerase},
owner = {to-file},
pmc = {PMC2447742},
pmid = {18420653},
pst = {ppublish},
timestamp = {2017-06-22},
}
@InProceedings{Sathanur2016,
author = {Sathanur, A V and Halappanavar, M},
title = {Influence Maximization on Complex Networks with Intrinsic Nodal Activation},
booktitle = {Under review},
year = {2016},
owner = {to-file},
timestamp = {2017-06-22},
}
@InProceedings{Sathanur2013,
author = {Sathanur, A V and Jandhyala, V and Xing, C},
title = {PHYSENSE: Scalable sociological interaction models for influence estimation on online social networks},
booktitle = {IEEE International Conference on Intelligence and Security Informatics},
year = {2013},
pages = {358--363},
organization = {IEEE},
owner = {to-file},
timestamp = {2017-06-22},
}
@Article{Humphrey1996,
author = {Humphrey, W and Dalke, A and Schulten, K},
title = {{VMD}: visual molecular dynamics},
journal = {Journal of Molecular Graphics},
year = {1996},
volume = {14},
number = {1},
pages = {33-8, 27-8},
owner = {to-file},
timestamp = {2017-06-27},
}
@Article{Dolinsky2007,
author = {Dolinsky, T J and Czodrowski, P and Li, Hui and Nielsen, J E and Jen, Jan H and Klebe, G and Baker, N A},
title = {{PDB2PQR}: expanding and upgrading automated preparation of biomolecular structures for molecular simulations},
journal = {Nucleic Acids Research},
year = {2007},
volume = {35},
pages = {W522-5},
bdsk-url-1 = {http://dx.doi.org/10.1093/nar/gkm276},
doi = {10.1093/nar/gkm276},
journal-full = {Nucleic acids research},
owner = {to-file},
timestamp = {2017-06-27},
}
@Article{Phillips2005,
author = {Phillips, J C and Braun, Rosemary and Wang, W and Gumbart, J and Tajkhorshid, E and Villa, E and Chipot, Christophe and Skeel, R D and Kal{\'e}, Laxmikant and Schulten, K},
title = {Scalable molecular dynamics with {NAMD}},
journal = {Journal of Computational Chemistry},
year = {2005},
volume = {26},
number = {16},
pages = {1781--802},
bdsk-url-1 = {http://dx.doi.org/10.1002/jcc.20289},
doi = {10.1002/jcc.20289},
owner = {to-file},
timestamp = {2017-06-22},
}
@Article{Leaver-Fay2011,
author = {Leaver-Fay, A and Tyka, M and Lewis, S M and Lange, O F and Thompson, J and Jacak, R and Kaufman, K and Renfrew, P D and Smith, C A and Sheffler, W and Davis, I W and Cooper, S and Treuille, A and Mandell, D J and Richter, F and Ban, Y A and Fleishman, S J and Corn, J E and Kim, D E and Lyskov, S and Berrondo, M and Mentzer, S and Popovi{\'c}, Z and Havranek, J J and Karanicolas, J and Das, R and Meiler, J and Kortemme, Tanja and Gray, J J and Kuhlman, B and Baker, D and Bradley, P},
title = {{ROSETTA3}: an object-oriented software suite for the simulation and design of macromolecules},
journal = {Methods in Enzymology},
year = {2011},
volume = {487},
pages = {545--74},
bdsk-url-1 = {http://dx.doi.org/10.1016/B978-0-12-381270-4.00019-6},
date-modified = {2016-05-12 13:37:07 +0000},
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