Works by Baker, Nathan

Results: 41

Differential geometry based solvation model II: Lagrangian formulation.

Published in:

Journal of Mathematical Biology, 2011, v. 63, n. 6, p. 1139, doi. 10.1007/s00285-011-0402-z

By:

Chen, Zhan;
Baker, Nathan;
Wei, G.

Publication type:

Article

Recovery or reorganisation? Long-term increases in riverine taxonomic and functional diversity are confounded by compositional dynamics.

Published in:

Hydrobiologia, 2025, v. 852, n. 7, p. 1693, doi. 10.1007/s10750-024-05665-5

By:

Baker, Nathan J.;
Pilotto, Francesca;
Welti, Ellen A. R.;
Osadčaja, Diana;
Palinauskas, Vaidas

Publication type:

Article

Multidecadal changes in functional diversity lag behind the recovery of taxonomic diversity.

Published in:

Ecology & Evolution (20457758), 2021, v. 11, n. 23, p. 17471, doi. 10.1002/ece3.8381

By:

Baker, Nathan Jay;
Pilotto, Francesca;
Haubrock, Phillip Joschka;
Beudert, Burkhard;
Haase, Peter

Publication type:

Article

Erratum to "Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models," by Jason Wagoner and Nathan A. Baker.

Published in:

2005

By:

Wagoner, Jason;
Baker, Nathan A.

Publication type:

Erratum

Jason Wagoner and Nathan A. Baker, "Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models," Journal of Computational Chemistry(2004) 25(13) 1623-1629.

Published in:

Journal of Computational Chemistry, 2004, v. 25, n. 14, p. 1801, doi. 10.1002/jcc.20108

By:

Wagoner, Jason;
Baker, Nathan A.

Publication type:

Article

Solvation forces on biomolecular structures: A comparison of explicit solvent and Poisson-Boltzmann models.

Published in:

Journal of Computational Chemistry, 2004, v. 25, n. 13, p. 1623, doi. 10.1002/jcc.20089

By:

Wagoner, Jason;
Baker, Nathan A.

Publication type:

Article

Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids.

Published in:

Biopolymers, 2006, v. 82, n. 2, p. 106, doi. 10.1002/bip.20409

By:

Konecny, Robert;
Trylska, Joanna;
Tama, Florence;
Zhang, Deqiang;
Baker, Nathan A.;
Brooks, Charles L.;
McCammon, J. A.

Publication type:

Article

Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach.

Published in:

Biopolymers, 2004, v. 75, n. 4, p. 325, doi. 10.1002/bip.20120

By:

Zhang, Deqiang;
Konecny, Robert;
Baker, Nathan A.;
McCammon, J. Andrew

Publication type:

Article

Long-term data reveal unimodal responses of ground beetle abundance to precipitation and land use but no changes in taxonomic and functional diversity.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-96910-7

By:

Zajicek, Petr;
Welti, Ellen A. R.;
Baker, Nathan J.;
Januschke, Kathrin;
Brauner, Oliver;
Haase, Peter

Publication type:

Article

APBSmem: A Graphical Interface for Electrostatic Calculations at the Membrane.

Published in:

PLoS ONE, 2010, v. 5, n. 9, p. 1, doi. 10.1371/journal.pone.0012722

By:

Callenberg, Keith M.;
Choudhary, Om P.;
de Forest, Gabriel L.;
Gohara, David W.;
Baker, Nathan A.;
Grabe, Michael

Publication type:

Article

Seasonal and spatial variation of stream macroinvertebrate taxonomic and functional diversity across three boreal regions.

Published in:

Insect Conservation & Diversity, 2023, v. 16, n. 2, p. 266, doi. 10.1111/icad.12623

By:

Baker, Nathan Jay;
Welti, Ellen A. R.;
Pilotto, Francesca;
Jourdan, Jonas;
Beudert, Burkhard;
Huttunen, Kaisa‐Leena;
Muotka, Timo;
Paavola, Riku;
Göthe, Emma;
Haase, Peter

Publication type:

Article

Using Language Science to Promote Interest in Science in a Science Museum.

Published in:

Visitor Studies, 2024, v. 27, n. 1, p. 19, doi. 10.1080/10645578.2023.2249759

By:

Patson, Nikole D.;
Baker, Nathan;
Awani, Sumurye;
Bednar, Nicholas;
Wagner, Laura

Publication type:

Article

Iron Responsive Element RNA Flexibility Described by NMR and Isotropic Reorientational Eigenmode Dynamics.

Published in:

Journal of Biomolecular NMR, 2005, v. 32, n. 3, p. 179, doi. 10.1007/s10858-005-7948-2

By:

Showalter, Scott A.;
Baker, Nathan A.;
Changguo Tang;
Hall, Kathleen B.

Publication type:

Article

Time series of freshwater macroinvertebrate abundances and site characteristics of European streams and rivers.

Published in:

Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-03445-3

By:

Welti, Ellen A. R.;
Bowler, Diana E.;
Sinclair, James S.;
Altermatt, Florian;
Álvarez-Cabria, Mario;
Amatulli, Giuseppe;
Angeler, David G.;
Archambaud, Gaït;
Arrate Jorrín, Iñaki;
Aspin, Thomas;
Azpiroz, Iker;
Baker, Nathan Jay;
Bañares, Iñaki;
Barquín Ortiz, José;
Bodin, Christian L.;
Bonacina, Luca;
Bonada, Núria;
Bottarin, Roberta;
Cañedo-Argüelles, Miguel;
Csabai, Zoltán

Publication type:

Article

ISA-TAB-Nano: A Specification for Sharing Nanomaterial Research Data in Spreadsheet-based Format.

Published in:

BMC Biotechnology, 2013, v. 12, n. 1, p. 1, doi. 10.1186/1472-6750-13-2

By:

Thomas, Dennis G.;
Gaheen, Sharon;
Harper, Stacey L.;
Fritts, Martin;
Klaessig, Fred;
Hahn-Dantona, Elizabeth;
Paik, David;
Pan, Sue;
Stafford, Grace A.;
Freund, Elaine T.;
Klemm, Juli D.;
Baker, Nathan A.

Publication type:

Article

Employee feedback technologies in the human performance system.

Published in:

Human Resource Development International, 2010, v. 13, n. 4, p. 477, doi. 10.1080/13678868.2010.501994

By:

Baker, Nathan

Publication type:

Article

Dynamical properties of fasciculin-2.

Published in:

Proteins, 1999, v. 36, n. 4, p. 447, doi. 10.1002/(SICI)1097-0134(19990901)36:4<447::AID-PROT8>3.0.CO;2-E

By:

Baker, Nathan A.;
Helms, Volkhard;
McCammon, J. Andrew

Publication type:

Article

Reproductive Success of Colonial Tree-nesting Waterbirds in Prairie Pothole Wetlands and Rivers throughout Northeastern South Dakota.

Published in:

American Midland Naturalist, 2015, v. 174, n. 1, p. 132, doi. 10.1674/0003-0031-174.1.132

By:

Baker, Nathan J.;
Dieter, Charles D.;
Bakker, Kristel K.

Publication type:

Article

ISIM: A Program for Grand Canonical Monte Carlo Simulations of the Ionic Environment of Biomolecules.

Published in:

Molecular Simulation, 2004, v. 30, n. 1, p. 45, doi. 10.1080/08927020310001597862

By:

Vitalis, Andreas;
Baker, Nathan A.;
McCammon, J. Andrew

Publication type:

Article

Predatory functional responses under increasing temperatures of two life stages of an invasive gecko.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-67194-0

By:

Haubrock, Phillip J.;
Cuthbert, Ross N.;
Veselý, Lukáš;
Balzani, Paride;
Baker, Nathan Jay;
Dick, Jaimie T. A.;
Kouba, Antonín

Publication type:

Article

Biomolecular electrostatics and solvation: a computational perspective.

Published in:

Quarterly Reviews of Biophysics, 2012, v. 45, n. 4, p. 427, doi. 10.1017/S003358351200011X

By:

Ren, Pengyu;
Chun, Jaehun;
Thomas, Dennis G.;
Schnieders, Michael J.;
Marucho, Marcelo;
Zhang, Jiajing;
Baker, Nathan A.

Publication type:

Article

Assessing the impact of technological change on similar occupations: Implications for employment alternatives.

Published in:

PLoS ONE, 2023, v. 18, n. 9, p. 1, doi. 10.1371/journal.pone.0291428

By:

Torosyan, Karine;
Wang, Sicheng;
Mack, Elizabeth A.;
Van Fossen, Jenna A.;
Baker, Nathan

Publication type:

Article

PB-AM: An open-source, fully analytical linear poisson-boltzmann solver.

Published in:

Journal of Computational Chemistry, 2017, v. 38, n. 15, p. 1275, doi. 10.1002/jcc.24528

By:

Felberg, Lisa E.;
Brookes, David H.;
Yap, Eng‐Hui;
Jurrus, Elizabeth;
Baker, Nathan A.;
Head‐Gordon, Teresa

Publication type:

Article

Parameterization of a geometric flow implicit solvation model.

Published in:

Journal of Computational Chemistry, 2013, v. 34, n. 8, p. 687, doi. 10.1002/jcc.23181

By:

Thomas, Dennis G.;
Chun, Jaehun;
Chen, Zhan;
Wei, Guowei;
Baker, Nathan A.

Publication type:

Article

Web servers and services for electrostatics calculations with APBS and PDB2PQR.

Published in:

Journal of Computational Chemistry, 2011, v. 32, n. 7, p. 1488, doi. 10.1002/jcc.21720

By:

Unni, Samir;
Huang, Yong;
Hanson, Robert M.;
Tobias, Malcolm;
Krishnan, Sriram;
Li, Wilfred W.;
Nielsen, Jens E.;
Baker, Nathan A.

Publication type:

Article

Helminth Parasites of Invasive Freshwater Fish in Lithuania.

Published in:

Animals (2076-2615), 2024, v. 14, n. 22, p. 3293, doi. 10.3390/ani14223293

By:

Kudlai, Olena;
Rakauskas, Vytautas;
Baker, Nathan Jay;
Pantoja, Camila;
Lisitsyna, Olga;
Binkienė, Rasa

Publication type:

Article

PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations.

Published in:

Nucleic Acids Research, 2004, v. 32, n. suppl 2, p. w665, doi. 10.1093/nar/gkh381

By:

Dolinsky, Todd J.;
Nielsen, Jens E.;
McCammon, J. Andrew;
Baker, Nathan A.

Publication type:

Article

Nanoinformatics: developing new computing applications for nanomedicine.

Published in:

Computing, 2012, v. 94, n. 6, p. 521, doi. 10.1007/s00607-012-0191-2

By:

Maojo, Victor;
Fritts, Martin;
Martin-Sanchez, Fernando;
De la Iglesia, Diana;
Cachau, Raul;
Garcia-Remesal, Miguel;
Crespo, Jose;
Mitchell, Joyce;
Anguita, Alberto;
Baker, Nathan;
Barreiro, Jose;
Benitez, Sonia;
De la Calle, Guillermo;
Facelli, Julio;
Ghazal, Peter;
Geissbuhler, Antoine;
Gonzalez-Nilo, Fernando;
Graf, Norbert;
Grangeat, Pierre;
Hermosilla, Isabel

Publication type:

Article

Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics.

Published in:

BMC Biophysics, 2015, v. 8, n. 1, p. 1, doi. 10.1186/s13628-015-0021-y

By:

Wenxiao Pan;
Daily, Michael;
Baker, Nathan A.

Publication type:

Article

Standardizing data.

Published in:

Nature Nanotechnology, 2013, v. 8, n. 2, p. 73, doi. 10.1038/nnano.2013.12

By:

Baker, Nathan A.;
Klemm, Juli D.;
Harper, Stacey L.;
Gaheen, Sharon;
Heiskanen, Mervi;
Rocca-Serra, Philippe;
Sansone, Susanna-Assunta

Publication type:

Article

Visualizing biomolecular electrostatics in virtual reality with UnityMol‐APBS.

Published in:

Protein Science: A Publication of the Protein Society, 2020, v. 29, n. 1, p. 237, doi. 10.1002/pro.3773

By:

Laureanti, Joseph;
Brandi, Juan;
Offor, Elvis;
Engel, David;
Rallo, Robert;
Ginovska, Bojana;
Martinez, Xavier;
Baaden, Marc;
Baker, Nathan A.

Publication type:

Article

The Moderating Effect of Scheduling Autonomy on Smartphone Use and Stress Among Older Workers.

Published in:

Work, Aging & Retirement, 2023, v. 9, n. 4, p. 329, doi. 10.1093/workar/waac017

By:

Fossen, Jenna A Van;
Baker, Nathan M;
Mack, Elizabeth A;
Chang, Chu-Hsiang;
Cotten, Shelia R;
Catalano, Isabella

Publication type:

Article

Why double-stranded RNA resists condensation.

Published in:

Nucleic Acids Research, 2014, v. 42, n. 16, p. 10823, doi. 10.1093/nar/gku756

By:

Tolokh, Igor S.;
Pabit, Suzette A.;
Katz, Andrea M.;
Chen, Yujie;
Drozdetski, Aleksander;
Baker, Nathan;
Pollack, Lois;
Onufriev, Alexey V.

Publication type:

Article

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations.

Published in:

Nucleic Acids Research, 2007, v. 35, n. suppl_2, p. W522, doi. 10.1093/nar/gkm276

By:

Dolinsky, Todd J.;
Czodrowski, Paul;
Li, Hui;
Nielsen, Jens E.;
Jensen, Jan H.;
Klebe, Gerhard;
Baker, Nathan A.

Publication type:

Article

Informatics and standards for nanomedicine technology.

Published in:

WIREs: Nanomedicine & Nanobiotechnology, 2011, v. 3, n. 5, p. 511, doi. 10.1002/wnan.152

By:

Thomas, Dennis G.;
Klaessig, Fred;
Harper, Stacey L.;
Fritts, Martin;
Hoover, Mark D.;
Gaheen, Sharon;
Stokes, Todd H.;
Reznik-Zellen, Rebecca;
Freund, Elaine T.;
Klemm, Juli D.;
Paik, David S.;
Baker, Nathan A.

Publication type:

Article

Metal accumulation in House Sparrow ( Passer domesticus ) from Thohoyandou, Limpopo province, South Africa.

Published in:

African Zoology, 2017, v. 52, n. 1, p. 43, doi. 10.1080/15627020.2017.1293491

By:

Baker, Nathan J;
Dahms, Simone;
Gerber, Ruan;
Maina, John;
Greenfield, Richard

Publication type:

Article

The physical basis of microtubule structure and stability.

Published in:

Protein Science: A Publication of the Protein Society, 2003, v. 12, n. 10, p. 2257, doi. 10.1110/ps.03187503

By:

Sept, David;
Baker, Nathan A.;
McCammon, J. Andrew

Publication type:

Article

Bayesian model aggregation for ensemble-based estimates of protein pKa values.

Published in:

Proteins, 2014, v. 82, n. 3, p. 354, doi. 10.1002/prot.24390

By:

Gosink, Luke J.;
Hogan, Emilie A.;
Pulsipher, Trenton C.;
Baker, Nathan A.

Publication type:

Article

On the development of protein p Ka calculation algorithms.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3287, doi. 10.1002/prot.23091

By:

Carstensen, Tommy;
Farrell, Damien;
Huang, Yong;
Baker, Nathan A.;
Nielsen, Jens Erik

Publication type:

Article

Progress in the prediction of p Ka values in proteins.

Published in:

Proteins, 2011, v. 79, n. 12, p. 3260, doi. 10.1002/prot.23189

By:

Alexov, Emil;
Mehler, Ernest L.;
Baker, Nathan;
M. Baptista, António;
Huang, Yong;
Milletti, Francesca;
Erik Nielsen, Jens;
Farrell, Damien;
Carstensen, Tommy;
Olsson, Mats H. M.;
Shen, Jana K.;
Warwicker, Jim;
Williams, Sarah;
Word, J. Michael

Publication type:

Article

TALL FIRS, ZIP-LINES, AND RESERVED INTEREST DEEDS: AN ASSESSMENT OF THE EFFECTIVENESS OF FEDERAL CONSERVATION EASEMENTS IN THE COLUMBIA RIVER GORGE NATIONAL SCENIC AREA.

Published in:

Environmental Law (Lewis & Clark Law School), 2016, v. 46, n. 4, p. 759

By:

Baker, Nathan J.;
Fraser, James A.

Publication type:

Article