CCP-SAS Covers

Monte Carlo simulation algorithm for B-DNA
Monte Carlo simulation algorithm for B-DNA
Solution structure of deglycosylated human IgG1 shows the role of CH2 glycans in its conformation.
Solution structure of deglycosylated human IgG1 shows the role of CH2 glycans in its conformation.
Solution structures of human myeloma IgG3 antibody reveal extended Fab and Fc regions relative to the other IgG subclasses.
Solution structures of human myeloma IgG3 antibody reveal extended Fab and Fc regions relative to the other IgG subclasses.
The solution structure of the heavy chain-only C5-Fc nanobody reveals exposed variable regions that are optimal for COVID-19 antigen interactions.
The solution structure of the heavy chain-only C5-Fc nanobody reveals exposed variable regions that are optimal for COVID-19 antigen interactions.

Publications arising from CCP-SAS software projects:

2025

E. Brookes, J. E. Curtis, A. Householder, M. Rocco

SAXS-A-FOLD: a website for fast ensemble modeling optimizing the fit of AlphaFold or user-supplied protein structures with flexible regions to SAXS data

Journal of Applied Crystallography, Vol. 58(3), pp. 1034-1049 (2025)

DOI

2024

Valentina A. Spiteri, James Doutch, Robert P. Rambo, Jayesh S. Bhatt, Jayesh Gor, Paul A. Dalby, Stephen J. Perkins

Using atomistic solution scattering modelling to elucidate the role of the Fc glycans in human IgG4

PLOS ONE, Vol. 19(4), pp. e0300964 (2024)

DOI PubMed

Sebastian Himbert, Dorian Gaboo, Emre Brookes, John F. Nagle, Maikel C. Rheinstädter

MEDUSA: A cloud-based tool for the analysis of X-ray diffuse scattering to obtain the bending modulus from oriented membrane stacks

PLOS Computational Biology, Vol. 20(1), pp. e1011749 (2024)

DOI

Xin Gao, Hina Iqbal, Ding-Quan Yu, Jayesh Gor, Alun R. Coker, Stephen J. Perkins

The SCR-17 and SCR-18 glycans in human complement factor H enhance its regulatory function

Journal of Biological Chemistry, Vol. 300(9) (2024)

DOI PubMed

2023

Gar Kay Hui, Xin Gao, Jayesh Gor, Jinghua Lu, Peter D. Sun, Stephen J. Perkins

The solution structure of the unbound IgG Fc receptor CD64 resembles its crystal structure: Implications for function

PloS One, Vol. 18(9), pp. e0288351 (2023)

DOI PubMed

Amy Y. Xu, Marco A. Blanco, Maria Monica Castellanos, Curtis W. Meuse, Kevin Mattison, Ioannis Karageorgos, Harold W. Hatch, Vincent K. Shen, Joseph E. Curtis

Role of Domain-Domain Interactions on the Self-Association and Physical Stability of Monoclonal Antibodies: Effect of pH and Salt

The Journal of Physical Chemistry. B, Vol. 127(39), pp. 8344-8357 (2023)

DOI PubMed

Amy Y. Xu, Marco A. Blanco, Maria Monica Castellanos, Curtis W. Meuse, Kevin Mattison, Ioannis Karageorgos, Harold W. Hatch, Vincent K. Shen, Joseph E. Curtis

Role of Domain-Domain Interactions on the Self-Association and Physical Stability of Monoclonal Antibodies: Effect of pH and Salt

The Journal of Physical Chemistry. B, Vol. 127(39), pp. 8344-8357 (2023)

DOI PubMed

Hina Iqbal, Ka Wai Fung, Jayesh Gor, Anthony C. Bishop, George I. Makhatadze, Barbara Brodsky, Stephen J. Perkins

A solution structure analysis reveals a bent collagen triple helix in the complement activation recognition molecule mannan-binding lectin

The Journal of Biological Chemistry, Vol. 299(2), pp. 102799 (2023)

DOI PubMed

Emre H. Brookes, Mattia Rocco

Beyond the US-SOMO-AF database: a new website for hydrodynamic, structural, and circular dichroism calculations on user-supplied structures

European biophysics journal: EBJ, Vol. 52(4-5), pp. 225-232 (2023)

DOI PubMed

Emre Brookes, Mattia Rocco, Patrice Vachette, Jill Trewhella

AlphaFold-predicted protein structures and small-angle X-ray scattering: insights from an extended examination of selected data in the Small-Angle Scattering Biological Data Bank

Journal of Applied Crystallography, Vol. 56(Pt 4), pp. 910-926 (2023)

DOI PubMed

Andreas Haahr Larsen, Emre Brookes, Martin Cramer Pedersen, Jacob Judas Kain Kirkensgaard

Shape2SAS: a web application to simulate small-angle scattering data and pair distance distributions from user-defined shapes

Journal of Applied Crystallography, Vol. 56(Pt 4), pp. 1287-1294 (2023)

DOI PubMed

Xin Gao, Joseph W. Thrush, Jayesh Gor, James H. Naismith, Raymond J. Owens, Stephen J. Perkins

The solution structure of the heavy chain–only C5-Fc nanobody reveals exposed variable regions that are optimal for COVID-19 antigen interactions

Journal of Biological Chemistry, Vol. 299(11) (2023)

DOI PubMed

2022

Frederik G. Tidemand, Sara Blemmer, Nicolai T. Johansen, Lise Arleth, Martin Cramer Pedersen

Non-ionic detergent assists formation of supercharged nanodiscs and insertion of membrane proteins

Biochimica Et Biophysica Acta. Biomembranes, Vol. 1864(6), pp. 183884 (2022)

DOI PubMed

Emre Brookes, Mattia Rocco

A database of calculated solution parameters for the AlphaFold predicted protein structures

Scientific Reports, Vol. 12(1), pp. 7349 (2022)

DOI

A. Barclay, N. Tidemand Johansen, F. G. Tidemand, L. Arleth, M. C. Pedersen

Global fitting of multiple data frames from SEC–SAXS to investigate the structure of next-generation nanodiscs

Acta Crystallographica Section D: Structural Biology, Vol. 78(4), pp. 483-493 (2022)

DOI

Christophe J. Lalaurie, Andrew Splevins, Teresa S. Barata, Karen A. Bunting, Daniel R. Higazi, Mire Zloh, Valentina A. Spiteri, Stephen J. Perkins, Paul A. Dalby

Elucidation of critical pH-dependent structural changes in Botulinum Neurotoxin E

Journal of Structural Biology, Vol. 214(3), pp. 107876 (2022)

DOI

J. Trewhella, P. Vachette, J. Bierma, C. Blanchet, E. Brookes, S. Chakravarthy, L. Chatzimagas, T. E. Cleveland, N. Cowieson, B. Crossett, A. P. Duff, D. Franke, F. Gabel, R. E. Gillilan, M. Graewert, A. Grishaev, J. M. Guss, M. Hammel, J. Hopkins, Q. Huang, J. S. Hub, G. L. Hura, T. C. Irving, C. M. Jeffries, C. Jeong, N. Kirby, S. Krueger, A. Martel, T. Matsui, N. Li, J. Pérez, L. Porcar, T. Prangé, I. Rajkovic, M. Rocco, D. J. Rosenberg, T. M. Ryan, S. Seifert, H. Sekiguchi, D. Svergun, S. Teixeira, A. Thureau, T. M. Weiss, A. E. Whitten, K. Wood, X. Zuo

A round-robin approach provides a detailed assessment of biomolecular small-angle scattering data reproducibility and yields consensus curves for benchmarking

Acta Crystallographica Section D: Structural Biology, Vol. 78(11), pp. 1315-1336 (2022)

DOI

Nicolai Tidemand Johansen, Marta Bonaccorsi, Tone Bengtsen, Andreas Haahr Larsen, Frederik Grønbæk Tidemand, Martin Cramer Pedersen, Pie Huda, Jens Berndtsson, Tamim Darwish, Nageshewar Rao Yepuri, Anne Martel, Thomas Günther Pomorski, Andrea Bertarello, Mark Sansom, Mikaela Rapp, Ramon Crehuet, Tobias Schubeis, Kresten Lindorff-Larsen, Guido Pintacuda, Lise Arleth, Lewis E Kay, Volker Dötsch

Mg2+-dependent conformational equilibria in CorA and an integrated view on transport regulation

eLife, Vol. 11, pp. e71887 (2022)

DOI

Cheol Jeong, Ryan Franklin, Karen J. Edler, Kenno Vanommeslaeghe, Susan Krueger, Joseph E. Curtis

Styrene–Maleic Acid Copolymer Nanodiscs to Determine the Shape of Membrane Proteins

The Journal of Physical Chemistry B, Vol. 126(5), pp. 1034-1044 (2022)

DOI

2021

T. Cleveland IV, E. Blick, S. Krueger, A. Leung, T. Darwish, P. Butler

Direct localization of detergents and bacteriorhodopsin in the lipidic cubic phase by small-angle neutron scattering

IUCrJ, Vol. 8(1), pp. 22-32 (2021)

DOI

Emilia C. Arturo, George W. Merkel, Michael R. Hansen, Sophia Lisowski, Deeanne Almeida, Kushol Gupta, Eileen K. Jaffe

Manipulation of a cation-π sandwich reveals conformational flexibility in phenylalanine hydroxylase

Biochimie, Vol. 183, pp. 63-77 (2021)

DOI

Jayesh Sonje, Seema Thakral, Susan Krueger, Raj Suryanarayanan

Reversible Self-Association in Lactate Dehydrogenase during Freeze–Thaw in Buffered Solutions Using Neutron Scattering

Molecular Pharmaceutics, Vol. 18(12), pp. 4459-4474 (2021)

DOI

Jakub Macošek, Bernd Simon, Johanna-Barbara Linse, Pravin Kumar Ankush Jagtap, Sophie L Winter, Jaelle Foot, Karine Lapouge, Kathryn Perez, Mandy Rettel, Miloš T Ivanović, Pawel Masiewicz, Brice Murciano, Mikhail M Savitski, Inga Loedige, Jochen S Hub, Frank Gabel, Janosch Hennig

Structure and dynamics of the quaternary hunchback mRNA translation repression complex

Nucleic Acids Research, Vol. 49(15), pp. 8866-8885 (2021)

DOI

Valentina A. Spiteri, Margaret Goodall, James Doutch, Robert P. Rambo, Jayesh Gor, Stephen J. Perkins

Solution structures of human myeloma IgG3 antibody reveal extended Fab and Fc regions relative to the other IgG subclasses

Journal of Biological Chemistry, Vol. 297(3) (2021)

DOI PubMed

Sergii Donets, Olga Guskova, Jens-Uwe Sommer

Searching for Aquamelt Behavior among Silklike Biomimetics during Fibrillation under Flow

The Journal of Physical Chemistry B, Vol. 125(12), pp. 3238-3250 (2021)

DOI

Orla M. Dunne, Xin Gao, Ruodan Nan, Jayesh Gor, Penelope J. Adamson, David L. Gordon, Martine Moulin, Michael Haertlein, V. Trevor Forsyth, Stephen J. Perkins

A Dimerization Site at SCR-17/18 in Factor H Clarifies a New Mechanism for Complement Regulatory Control

Frontiers in Immunology, Vol. 11 (2021)

Valentina A. Spiteri, James Doutch, Robert P. Rambo, Jayesh Gor, Paul A. Dalby, Stephen J. Perkins

Solution structure of deglycosylated human IgG1 shows the role of CH2 glycans in its conformation

Biophysical Journal, Vol. 120(9), pp. 1814-1834 (2021)

DOI

A. H. Larsen, M. C. Pedersen

Experimental noise in small-angle scattering can be assessed using the Bayesian indirect Fourier transformation

Journal of Applied Crystallography, Vol. 54(5), pp. 1281-1289 (2021)

DOI

Andreas Haahr Larsen, Nicolai Tidemand Johansen, Michael Gajhede, Lise Arleth, Søren Roi Midtgaard

Lipid-bound ApoE3 self-assemble into elliptical disc-shaped particles

Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1863(1), pp. 183495 (2021)

DOI

Alexandra S. Solovyova, Daniel T. Peters, Gema Dura, Helen Waller, Jeremy H. Lakey, David A. Fulton

Probing the oligomeric re-assembling of bacterial fimbriae in vitro: a small-angle X-ray scattering and analytical ultracentrifugation study

European Biophysics Journal, Vol. 50(3), pp. 597-611 (2021)

DOI

Frank Heinrich, Que N. Van, Frantz Jean-Francois, Andrew G. Stephen, Mathias Lösche

Membrane-bound KRAS approximates an entropic ensemble of configurations

Biophysical Journal, Vol. 120(18), pp. 4055-4066 (2021)

DOI

Luke A. Perera, Steffen Preissler, Nathan R. Zaccai, Sylvain Prévost, Juliette M. Devos, Michael Haertlein, David Ron

Structures of a deAMPylation complex rationalise the switch between antagonistic catalytic activities of FICD

Nature Communications, Vol. 12(1), pp. 5004 (2021)

DOI

2020

Prasad Calyam, Nancy Wilkins‐Diehr, Mark Miller, Emre H. Brookes, Ritu Arora, Amit Chourasia, Douglas M. Jennewein, Viswanath Nandigam, M. Drew LaMar, Sean B. Cleveland, Greg Newman, Shaowen Wang, Ilya Zaslavsky, Michael A. Cianfrocco, Kevin Ellett, David Tarboton, Keith G. Jeffery, Zhiming Zhao, Juan González‐Aranda, Mark J. Perri, Greg Tucker, Leonardo Candela, Tamas Kiss, Sandra Gesing

Measuring success for a future vision: Defining impact in science gateways/virtual research environments

Concurrency and Computation: Practice and Experience, pp. cpe.6099 (2020)

DOI

Nilufar Kadkhodayi-Kholghi, Jayesh S. Bhatt, Jayesh Gor, Lindsay C. McDermott, Daniel P. Gale, Stephen J. Perkins

The solution structure of the complement deregulator FHR5 reveals a compact dimer and provides new insights into CFHR5 nephropathy

Journal of Biological Chemistry, Vol. 295(48), pp. 16342-16358 (2020)

DOI

Dagan C. Marx, Mathis J. Leblanc, Ashlee M. Plummer, Susan Krueger, Karen G. Fleming

Domain interactions determine the conformational ensemble of the periplasmic chaperone SurA

Protein Science, Vol. 29(10), pp. 2043-2053 (2020)

DOI

Dagan C. Marx, Ashlee M. Plummer, Anneliese M. Faustino, Taylor Devlin, Michaela A. Roskopf, Mathis J. Leblanc, Henry J. Lessen, Barbara T. Amann, Patrick J. Fleming, Susan Krueger, Stephen D. Fried, Karen G. Fleming

SurA is a cryptically grooved chaperone that expands unfolded outer membrane proteins

Proceedings of the National Academy of Sciences, Vol. 117(45), pp. 28026-28035 (2020)

DOI

Andrew J. Boughton, Susan Krueger, David Fushman

Branching via K11 and K48 Bestows Ubiquitin Chains with a Unique Interdomain Interface and Enhanced Affinity for Proteasomal Subunit Rpn1

Structure, Vol. 28(1), pp. 29-43.e6 (2020)

DOI PubMed

Rahul Saxena, Christopher B. Stanley, Pankaj Kumar, Matthew J. Cuneo, Digvijay Patil, Jyoti Jha, Kevin L. Weiss, Dhruba K. Chattoraj, Elliott Crooke

A nucleotide-dependent oligomerization of the Escherichia coli replication initiator DnaA requires residue His136 for remodeling of the chromosomal origin

Nucleic Acids Research, Vol. 48(1), pp. 200-211 (2020)

DOI

Trey A. Ronnebaum, Kushol Gupta, David W. Christianson

Higher-order oligomerization of a chimeric αβγ bifunctional diterpene synthase with prenyltransferase and class II cyclase activities is concentration-dependent

Journal of Structural Biology, Vol. 210(1), pp. 107463 (2020)

DOI

2019

Samuel Bowerman, Joseph E. Curtis, Joseph Clayton, Emre H. Brookes, Jeff Wereszczynski

BEES: Bayesian Ensemble Estimation from SAS

Biophysical Journal, Vol. 117(3), pp. 399-407 (2019)

DOI PubMed

Andrew R. McCluskey, Adrian Sanchez-Fernandez, Karen J. Edler, Stephen C. Parker, Andrew J. Jackson, Richard A. Campbell, Thomas Arnold

Bayesian determination of the effect of a deep eutectic solvent on the structure of lipid monolayers

Physical Chemistry Chemical Physics, Vol. 21(11), pp. 6133-6141 (2019)

DOI

Nuria Codina, David Hilton, Cheng Zhang, Nesrine Chakroun, Shahina S. Ahmad, Stephen J. Perkins, Paul A. Dalby

An Expanded Conformation of an Antibody Fab Region by X-Ray Scattering, Molecular Dynamics, and smFRET Identifies an Aggregation Mechanism

Journal of Molecular Biology, Vol. 431(7), pp. 1409-1425 (2019)

DOI

A. R. McCluskey, J. Grant, A. R. Symington, T. Snow, J. Doutch, B. J. Morgan, S. C. Parker, K. J. Edler

An introduction to classical molecular dynamics simulation for experimental scattering users

Journal of Applied Crystallography, Vol. 52(3), pp. 665-668 (2019)

DOI

Alexey Savelyev, Emre Brookes

GenApp: Extensible tool for rapid generation of web and native GUI applications

Future Generation Computer Systems, Vol. 94, pp. 929-936 (2019)

DOI

Gar Kay Hui, Antoni D. Gardener, Halima Begum, Charles Eldrid, Konstantinos Thalassinos, Jayesh Gor, Stephen J. Perkins

The solution structure of the human IgG2 subclass is distinct from those for human IgG1 and IgG4 providing an explanation for their discrete functions

Journal of Biological Chemistry, Vol. 294(28), pp. 10789-10806 (2019)

DOI PubMed

A. R. McCluskey, J. Grant, A. J. Smith, J. L. Rawle, D. J. Barlow, M. J. Lawrence, S. C. Parker, K. J. Edler

Assessing molecular simulation for the analysis of lipid monolayer reflectometry

Journal of Physics Communications, Vol. 3(7), pp. 075001 (2019)

DOI

David W. Wright, Emma L.K. Elliston, Gar Kay Hui, Stephen J. Perkins

Atomistic Modeling of Scattering Curves for Human IgG1/4 Reveals New Structure-Function Insights

Biophysical Journal, Vol. 117(11), pp. 2101-2119 (2019)

DOI

Emre Brookes, Joe Stubbs

GenApp, Containers and Abaco: Technical Paper

PEARC '19, pp. 1–8 (2019)

DOI

Martin Bush, Bashir M. Alhanshali, Shuo Qian, Christopher B. Stanley, William T. Heller, Tsutomu Matsui, Thomas M. Weiss, Iain D. Nicholl, Thomas Walz, David J. E. Callaway, Zimei Bu

An ensemble of flexible conformations underlies mechanotransduction by the cadherin–catenin adhesion complex

Proceedings of the National Academy of Sciences, Vol. 116(43), pp. 21545-21555 (2019)

DOI PubMed

Letitia O. Puster, Christopher B. Stanley, Vladimir N. Uversky, Joseph E. Curtis, Susan Krueger, Yuzhuo Chu, Cynthia B. Peterson

Characterization of an Extensive Interface on Vitronectin for Binding to Plasminogen Activator Inhibitor-1: Adoption of Structure in an Intrinsically Disordered Region

Biochemistry, Vol. 58(51), pp. 5117-5134 (2019)

DOI

Amy Yuanyuan Xu, Maria Monica Castellanos, Kevin Mattison, Susan Krueger, Joseph E. Curtis

Studying Excipient Modulated Physical Stability and Viscosity of Monoclonal Antibody Formulations Using Small-Angle Scattering

Molecular Pharmaceutics, Vol. 16(10), pp. 4319-4338 (2019)

DOI

2018

Maria Monica Castellanos, Steven C. Howell, D. Travis Gallagher, Joseph E. Curtis

Characterization of the NISTmAb Reference Material using small-angle scattering and molecular simulation

Analytical and Bioanalytical Chemistry, Vol. 410(8), pp. 2141-2159 (2018)

DOI

Maria Monica Castellanos, Kevin Mattison, Susan Krueger, Joseph E. Curtis

Characterization of the NISTmAb Reference Material using small-angle scattering and molecular simulation

Analytical and Bioanalytical Chemistry, Vol. 410(8), pp. 2161-2171 (2018)

DOI

Emre Brookes, Mattia Rocco

Recent advances in the UltraScan SOlution MOdeller (US-SOMO) hydrodynamic and small-angle scattering data analysis and simulation suite

European Biophysics Journal, Vol. 47(7), pp. 855-864 (2018)

DOI

Andrew McCluskey, Benjamin Morgan, Karen Edler, Stephen Parker

pylj: A teaching tool for classical atomistic simulation

Journal of Open Source Education, Vol. 2(16), pp. 19 (2018)

DOI

Amy J. Osborne, Ruodan Nan, Ami Miller, Jayesh S. Bhatt, Jayesh Gor, Stephen J. Perkins

Two distinct conformations of factor H regulate discrete complement-binding functions in the fluid phase and at cell surfaces

Journal of Biological Chemistry, Vol. 293(44), pp. 17166-17187 (2018)

DOI PubMed

2017

Ruodan Nan, Christopher M. Furze, David W. Wright, Jayesh Gor, Russell Wallis, Stephen J. Perkins

Flexibility in Mannan-Binding Lectin-Associated Serine Proteases-1 and-2 Provides Insight on Lectin Pathway Activation

Structure, Vol. 25(2), pp. 364-375 (2017)

DOI

Kenneth T. Walker, Ruodan Nan, David W. Wright, Jayesh Gor, Anthony C. Bishop, George I. Makhatadze, Barbara Brodsky, Stephen J. Perkins

Non-linearity of the collagen triple helix in solution and implications for collagen function

Biochemical Journal, Vol. 474, pp. 2203-2217 (2017)

DOI

Maria Monica Castellanos, Arnold McAuley, Joseph E. Curtis

Investigating Structure and Dynamics of Proteins in Amorphous Phases Using Neutron Scattering

Computational and Structural Biotechnology Journal, Vol. 15, pp. 117-130 (2017)

DOI

Purva P. Bhojane, Michael R. Duff, Khushboo Bafna, Pratul Agarwal, Christopher Stanley, Elizabeth E. Howell

Small Angle Neutron Scattering Studies of R67 Dihydrofolate Reductase, a Tetrameric Protein with Intrinsically Disordered N-Termini

Biochemistry, Vol. 56(44), pp. 5886-5899 (2017)

DOI

Maria Monica Castellanos, James A. Snyder, Melody Lee, Srinivas Chakravarthy, Nicholas J. Clark, Arnold McAuley, Joseph E. Curtis

Characterization of Monoclonal Antibody-Protein Antigen Complexes Using Small-Angle Scattering and Molecular Modeling

Antibodies, Vol. 6(4), pp. 25 (2017)

DOI

Weihong Zhang, Steven C. Howell, David W. Wright, Andrew Heindel, Xiangyun Qiu, Jianhan Chen, Joseph E. Curtis

Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates

Journal of Molecular Graphics & Modelling, Vol. 73, pp. 179-190 (2017)

DOI

2016

Nathan R. Zaccai, Clifford W. Sandlin, James T. Hoopes, Joseph E. Curtis, Patrick J. Fleming, Karen G. Fleming, Susan Krueger, Z. Kelman

Deuterium Labeling Together with Contrast Variation Small-Angle Neutron Scattering Suggests How Skp Captures and Releases Unfolded Outer Membrane Proteins

, Vol. 566, pp. 159-210 (2016)

Travis Eisemann, Michael McCauley, Marie-France Langelier, Kushol Gupta, Swati Roy, Gregory D. Van Duyne, John M. Pascal

Tankyrase-1 Ankyrin Repeats Form an Adaptable Binding Platform for Targets of ADP-Ribose Modification

Structure, Vol. 24(10), pp. 1679-1692 (2016)

DOI

Emre H. Brookes, Abhishek Kapoor, Priyanshu Patra, Suresh Marru, Raminder Singh, Marlon Pierce

GSoC 2015 student contributions to GenApp and Airavata

Concurrency and Computation: Practice and Experience, Vol. 28(7), pp. 1960-1970 (2016)

DOI

Kuo Hao Lee, Jianhan Chen

Multiscale enhanced sampling of intrinsically disordered protein conformations

Journal of Computational Chemistry, Vol. 37(6), pp. 550-557 (2016)

DOI

Carlos A. Castaneda, Emma K. Dixon, Olivier Walker, Apurva Chaturvedi, Mark A. Nakasone, Joseph E. Curtis, Megan R. Reed, Susan Krueger, T. Ashton Cropp, David Fushman

Linkage via K27 Bestows Ubiquitin Chains with Unique Properties among Polyubiquitins

Structure, Vol. 24(3), pp. 423-436 (2016)

DOI

Carlos A. Castaneda, Apurva Chaturvedi, Christina M. Camara, Joseph E. Curtis, Susan Krueger, David Fushman

Linkage-specific conformational ensembles of non-canonical polyubiquitin chains

Physical Chemistry Chemical Physics, Vol. 18(8), pp. 5771-5788 (2016)

DOI

Henna Zahid, Layeque Miah, Andy M. Lau, Lea Brochard, Debolina Hati, Tam T. T. Bui, Alex F. Drake, Jayesh Gor, Stephen J. Perkins, Lindsay C. McDermott

Zinc-induced oligomerization of zinc α2 glycoprotein reveals multiple fatty acid-binding sites

Biochemical Journal, Vol. 473(1), pp. 43-54 (2016)

DOI

Matthew Green, Louise Hatter, Emre Brookes, Panos Soultanas, David J. Scott

Defining the Intrinsically Disordered C-Terminal Domain of SSB Reveals DNA-Mediated Compaction

Journal of Molecular Biology, Vol. 428(2), pp. 357-364 (2016)

DOI

Zhiguang Jia, Jianhan Chen

Necessity of high-resolution for coarse-grained modeling of flexible proteins

Journal of Computational Chemistry, Vol. 37(18), pp. 1725-1733 (2016)

DOI

Steven C. Howell, Xiangyun Qiu, Joseph E. Curtis

Monte Carlo simulation algorithm for B-DNA

Journal of Computational Chemistry, Vol. 37(29), pp. 2553-2563 (2016)

DOI

S. J. Perkins, D. W. Wright, H. Zhang, E. H. Brookes, J. Chen, T. C. Irving, S. Krueger, D. J. Barlow, K. J. Edler, D. J. Scott, N. J. Terrill, S. M. King, P. D. Butler, J. E. Curtis

Atomistic modelling of scattering data in the Collaborative Computational Project for Small Angle Scattering (CCP-SAS)

Journal of Applied Crystallography, Vol. 49(6), pp. 1861-1875 (2016)

DOI

Maria Monica Castellanos, Nicholas J. Clark, Max C. Watson, Susan Krueger, Arnold McAuley, Joseph E. Curtis

Role of Molecular Flexibility and Colloidal Descriptions of Proteins in Crowded Environments from Small-Angle Scattering

The Journal of Physical Chemistry B, Vol. 120(49), pp. 12511-12518 (2016)

DOI

Emre Brookes, Patrice Vachette, Mattia Rocco, Javier Perez

US-SOMO HPLC-SAXS module: dealing with capillary fouling and extraction of pure component patterns from poorly resolved SEC-SAXS data

Journal of Applied Crystallography, Vol. 49, pp. 1827-1841 (2016)

DOI

Ka Wai Fung, David W. Wright, Jayesh Gor, Marcus J. Swann, Stephen J. Perkins

Domain structure of human complement C4b extends with increasing NaCl concentration: implications for its regulatory mechanism

Biochemical Journal, Vol. 473, pp. 4473-4491 (2016)

DOI

Zhiguang Jia, Susan K. Whitaker, John M. Tomich, Jianhan Chen

Organization and Structure of Branched Amphipathic Oligopeptide Bilayers

Langmuir, Vol. 32(38), pp. 9883-9891 (2016)

DOI

2015

Elizabeth Rodriguez, Ruodan Nan, Keying Li, Jayesh Gor, Stephen J. Perkins

A Revised Mechanism for the Activation of Complement C3 to C3b A MOLECULAR EXPLANATION OF A DISEASE-ASSOCIATED POLYMORPHISM

Journal of Biological Chemistry, Vol. 290(4), pp. 2334-2350 (2015)

DOI

David W. Wright, Stephen J. Perkins

SCT: a suite of programs for comparing atomistic models with small-angle scattering data

Journal of Applied Crystallography, Vol. 48, pp. 953-961 (2015)

DOI

Huaying Zhao, Rodolfo Ghirlando, Carlos Alfonso, Fumio Arisaka, Ilan Attali, David L. Bain, Marina M. Bakhtina, Donald F. Becker, Gregory J. Bedwell, Ahmet Bekdemir, Tabot M. D. Besong, Catherine Birck, Chad A. Brautigam, William Brennerman, Olwyn Byron, Agnieszka Bzowska, Jonathan B. Chaires, Catherine T. Chaton, Helmut Coelfen, Keith D. Connaghan, Kimberly A. Crowley, Ute Curth, Tina Daviter, William L. Dean, Ana I. Diez, Christine Ebel, Debra M. Eckert, Leslie E. Eisele, Edward Eisenstein, Patrick England, Carlos Escalante, Jeffrey A. Fagan, Robert Fairman, Ron M. Finn, Wolfgang Fischle, Jose Garcia de la Torre, Jayesh Gor, Henning Gustafsson, Damien Hall, Stephen E. Harding, Jose G. Hernandez Cifre, Andrew B. Herr, Elizabeth E. Howell, Richard S. Isaac, Shu-Chuan Jao, Davis Jose, Soon-Jong Kim, Bashkim Kokona, Jack A. Kornblatt, Dalibor Kosek, Elena Krayukhina, Daniel Krzizike, Eric A. Kusznir, Hyewon Kwon, Adam Larson, Thomas M. Laue, Aline Le Roy, Andrew P. Leech, Hauke Lilie, Karolin Luger, Juan R. Luque-Ortega, Jia Ma, Carrie A. May, Ernest L. Maynard, Anna Modrak-Wojcik, Yee-Foong Mok, Norbert Muecke, Luitgard Nagel-Steger, Geeta J. Narlikar, Masanori Noda, Amanda Nourse, Tomas Obsil, Chad K. Park, Jin-Ku Park, Peter D. Pawelek, Erby E. Perdue, Stephen J. Perkins, Matthew A. Perugini, Craig L. Peterson, Martin G. Peverelli, Grzegorz Piszczek, Gali Prag, Peter E. Prevelige, Bertrand D. E. Raynal, Lenka Rezabkova, Klaus Richter, Alison E. Ringel, Rose Rosenberg, Arthur J. Rowe, Arne C. Rufer, David J. Scott, Javier G. Seravalli, Alexandra S. Solovyova, Renjie Song, David Staunton, Caitlin Stoddard, Katherine Stott, Holger M. Strauss, Werner W. Streicher, John P. Sumida, Sarah G. Swygert, Roman H. Szczepanowski, Ingrid Tessmer, Ronald T. Toth, Ashutosh Tripathy, Susumu Uchiyama, Stephan F. W. Uebel, Satoru Unzai, Anna Vitlin Gruber, Peter H. von Hippel, Christine Wandrey, Szu-Huan Wang, Steven E. Weitzel, Beata Wielgus-Kutrowska, Cynthia Wolberger, Martin Wolff, Edward Wright, Yu-Sung Wu, Jacinta M. Wubben, Peter Schuck

A Multilaboratory Comparison of Calibration Accuracy and the Performance of External References in Analytical Ultracentrifugation

Plos One, Vol. 10(5), pp. e0126420 (2015)

DOI

Lucy E. Rayner, Gar Kay Hui, Jayesh Gor, Richard K. Heenan, Paul A. Dalby, Stephen J. Perkins

The Solution Structures of Two Human IgG1 Antibodies Show Conformational Stability and Accommodate Their C1q and Fc gamma R Ligands

Journal of Biological Chemistry, Vol. 290(13), pp. 8420-8438 (2015)

DOI

Emre H. Brookes, Nadeem Anjum, Joseph E. Curtis, Suresh Marru, Raminder Singh, Marlon Pierce

The GenApp framework integrated with Airavata for managed compute resource submissions

Concurrency and Computation: Practice and Experience, Vol. 27(16), pp. 4292-4303 (2015)

DOI

Barbara J. Tarasevich, John S. Philo, Nasib Karl Maluf, Susan Krueger, Garry W. Buchko, Genyao Lin, Wendy J. Shaw

The leucine-rich amelogenin protein (LRAP) is primarily monomeric and unstructured in physiological solution

Journal of Structural Biology, Vol. 190(1), pp. 81-91 (2015)

DOI

David W. Wright, Ruodan Nan, Gar-Kay Hui, Joseph E. Curtis, Emre H. Brookes, Stephen J. Perkins

CCP-SAS - Novel Approaches for the Atomistic Modelling of Small Angle Scattering Data in Biology

Biophysical Journal, Vol. 108(2), pp. 191A-191A (2015)

DOI

Gar Kay Hui, David W. Wright, Owen L. Vennard, Lucy E. Rayner, Melisa Pang, See Cheng Yeo, Jayesh Gor, Karen Molyneux, Jonathan Barratt, Stephen J. Perkins

The solution structures of native and patient monomeric human IgA1 reveal asymmetric extended structures: implications for function and IgAN disease

Biochemical Journal, Vol. 471, pp. 167-185 (2015)

DOI

2014

Zhe Zhang, Jan-Michael Y. Carrillo, Suk-kyun Ahn, Bin Wu, Kunlun Hong, Gregory S. Smith, Changwoo Do

Atomistic Structure of Bottlebrush Polymers: Simulations and Neutron Scattering Studies

Macromolecules, Vol. 47(16), pp. 5808-5814 (2014)

DOI

Stephen J. Perkins, Ka Wai Fung, Sanaullah Khan

Molecular interactions between complement factor H and its heparin and heparan sulfate ligands

Frontiers in Immunology, Vol. 5, pp. 126 (2014)

DOI

Eric J. Yearley, Paul D. Godfrin, Tatiana Perevozchikova, Hailiang Zhang, Peter Falus, Lionel Porcar, Michihiro Nagao, Joseph E. Curtis, Pradad Gawande, Rosalynn Taing, Isidro E. Zarraga, Norman J. Wagner, Yun Liu

Observation of Small Cluster Formation in Concentrated Monoclonal Antibody Solutions and Its Implications to Solution Viscosity

Biophysical Journal, Vol. 106(8), pp. 1763-1770 (2014)

DOI

Max C. Watson, Joseph E. Curtis

Probing the Average Local Structure of Biomolecules Using Small-Angle Scattering and Scaling Laws

Biophysical Journal, Vol. 106(11), pp. 2474-2482 (2014)

DOI

Nicholas J. Clark, Madushi Raththagala, Nathan T. Wright, Elizabeth A. Buenger, Joel F. Schildbach, Susan Krueger, Joseph E. Curtis

Structures of TraI in solution

Journal of Molecular Modeling, Vol. 20(6), pp. 2308 (2014)

DOI

Joseph E. Curtis, Hailiang Zhang, Hirsh Nanda

SLDMOL: A tool for the structural characterization of thermally disordered membrane proteins

Computer Physics Communications, Vol. 185(11), pp. 3010-3015 (2014)

DOI

Susan Krueger, Jae-Ho Shin, Joseph E. Curtis, Kenneth A. Rubinson, Zvi Kelman

The solution structure of full-length dodecameric MCM by SANS and molecular modeling

Proteins: Structure, Function, and Bioinformatics, Vol. 82(10), pp. 2364-2374 (2014)

DOI

Yi Peng, Joseph E. Curtis, Xianyang Fang, Sarah A. Woodson

Structural model of an mRNA in complex with the bacterial chaperone Hfq

Proceedings of the National Academy of Sciences of the United States of America, Vol. 111(48), pp. 17134-17139 (2014)

DOI

Weihong Zhang, Jianhan Chen

Replica exchange with guided annealing for accelerated sampling of disordered protein conformations

Journal of Computational Chemistry, Vol. 35(23), pp. 1682-1689 (2014)

DOI

Lucy E. Rayner, Gar Kay Hui, Jayesh Gor, Richard K. Heenan, Paul A. Dalby, Stephen J. Perkins

The Fab Conformations in the Solution Structure of Human Immunoglobulin G4 (IgG4) Restrict Access to Its Fc Region IMPLICATIONS FOR FUNCTIONAL ACTIVITY

Journal of Biological Chemistry, Vol. 289(30), pp. 20740-20756 (2014)

DOI

2013

M. C. Watson, J. E. Curtis

Rapid and accurate calculation of small-angle scattering profiles using the golden ratio

Journal of Applied Crystallography, Vol. 46(4), pp. 1171-1177 (2013)

DOI

Hailiang Zhang, Sheila Khodadadi, Steven L. Fiedler, Joseph E. Curtis

Role of Water and Ions on the Dynamical Transition of RNA

The Journal of Physical Chemistry Letters, Vol. 4(19), pp. 3325-3329 (2013)

DOI

K. L. Sarachan, J. E. Curtis, S. Krueger

Small-angle scattering contrast calculator for protein and nucleic acid complexes in solution

Journal of Applied Crystallography, Vol. 46(6), pp. 1889-1893 (2013)

DOI

Nicholas J. Clark, Hailiang Zhang, Susan Krueger, Hyo Jin Lee, Randal R. Ketchem, Bruce Kerwin, Sekhar R. Kanapuram, Michael J. Treuheit, Arnold McAuley, Joseph E. Curtis

Small-Angle Neutron Scattering Study of a Monoclonal Antibody Using Free-Energy Constraints

The Journal of Physical Chemistry B, Vol. 117(45), pp. 14029-14038 (2013)

DOI

Emre Brookes, Javier Perez, Barbara Cardinali, Aldo Profumo, Patrice Vachette, Mattia Rocco

Fibrinogen species as resolved by HPLC-SAXS data processing within the UltraScan Solution Modeler (US-SOMO) enhanced SAS module

Journal of Applied Crystallography, Vol. 46, pp. 1823-1833 (2013)

DOI

Lucy E. Rayner, Nilufar Kadkhodayi-Kholghi, Richard K. Heenan, Jayesh Gor, Paul A. Dalby, Stephen J. Perkins

The Solution Structure of Rabbit IgG Accounts for Its Interactions with the Fc Receptor and Complement C1q and Its Conformational Stability

Journal of Molecular Biology, Vol. 425(3), pp. 506-523 (2013)

DOI

Sanaullah Khan, Ka Wai Fung, Elizabeth Rodriguez, Rima Patel, Jayesh Gor, Barbara Mulloy, Stephen J. Perkins

The Solution Structure of Heparan Sulfate Differs from That of Heparin IMPLICATIONS FOR FUNCTION

Journal of Biological Chemistry, Vol. 288(39), pp. 27737-27751 (2013)

DOI

Presentations given on CCP-SAS software and its applications:

2019

  • Y. Chen, C. Jeong, A. Savelyev, S.nKrueger, J. E. Curtis, E. H. Brookes, D. Fushman. ROTDIF-web and ALTENS: GenApp-based Science Gateways for Biomolecular Nuclear Magnetic Resonance (NMR) Data Analysis and Structure Modeling. Gateways 2019. San Diego, California. September 23-25, 2019. DOI: 10.17605/OSF.IO/T4GKH
  • M. Christie, M. Owczarzak, Y-S. Ho, P. Parsons, S. Krueger, J. E. Curtis, E. H. Brookes. GenApp Style and Layout Enhancements. Gateways 2019. San Diego, California. September 23-25, 2019. DOI: 10.17605/OSF.IO/NQSPR. Poster
  • A. Chourasia, D. Nedau, J. Luo, T. Chen, M. Miller, E. Brookes. Enabling rich data sharing for Science Gateways via the SeedMeLab platform. Gateways 2019. San Diego, California. September 23-25, 2019. DOI: 10.17605/OSF.IO/WV3BF
  • N. Wilkins-Diehr, M. Miller, E. H. Brookes, R. Arora, A. Chourasia, P. Calyam, D. M. Jennewein, V. Nandigam, M. D. LaMar, S. B. Cleveland, G. Newman, S. Wang, I. Zaslavsky, M. A. Cianfrocco, K. Ellett, D. Tarboton. Measuring Success: How Science Gateways Define Impact. Gateways 2019. San Diego, California. September 23-25, 2019.
  • C. Jeong, P. Vachette, E. H. Brookes. MultiSAXSHub: A GenApp-Generated Science Gateway for Unified Computational SAXS Modeling Tool. Gateways 2019. San Diego, California. September 23-25, 2019. DOI: 10.17605/OSF.IO/354CJ17. Poster
  • A Guan, M. Casertano, C. Jeong, E. H. Brookes, D. Fushman. A GenApp-Generated Science Gateway for Comprehensive Analysis of Paramagnetic Effects in Biomolecular NMR Data. Gateways 2019. San Diego, California. September 23-25, 2019. DOI: 10.17605/OSF.IO/92VCY.
  • G. K. Hui, A. D. Gardener, H. Begum, J. Gor, S. J. Perkins. The solution structure of the human IgG2 subclass is distinct from those for human IgG1 and IgG4, providing an explanation for their discrete functions. 24th International Analytical Ultracentrifugation Workshop and Symposium. Christchurch, New Zealand, August 24-29, 2019.
  • V. A. Spiteri, C. F. S. Eldrid, J. Doutch, R. P. Rambo, J. Gor, K. Thalassinos, P. A. Dalby, S. J. Perkins. Unravelling the solution structures and stabilities of therapeutic antibodies with and without glycans. 24th International Analytical Ultracentrifugation Workshop and Symposium. Christchurch, New Zealand, August 24-29, 2019.
  • E. Brookes, J. Stubbs. GenApp, Containers and Abaco. PEARC19 Practice and Experience in Advanced Research Computing: RISE OF THE MACHINES [learning]. Chicago, Ill. July 29-August 1, 2019.
  • K. Edler - Micelles & Monolayers: Exploring use of models to understand scattering data. CECAM - Simulations of Small angle scattering for soft matter and life sciences. Institut-Laue-Langevin, Grenoble, France. 8-12 April 2019
  • S. Perkins, J. Bhatt — CCP-SAS - a community consortium for the advanced modelling of scattering data - applications and implementation. CECAM - Simulations of Small angle scattering for soft matter and life sciences. Institut-Laue-Langevin, Grenoble, France. 8-12 April 2019
  • J. Clayton, J. Wereszczynski. Using goal-oriented enhanced sampling to understand SAXS and NMR data of IsdH from Staphylococcus aureus. 63rd Annual Meeting of the Biophysical Society, March 2-6, 2019, Baltimore Maryland, USA. Poster
  • J. Wereszczynski - Exploring the Relationship Between the Structure, Function, and Dynamics of Biomolecular Complexes - University of Delaware Department of Physics, February 2019
  • J. Wereszczynski - Exploring the Relationship Between the Structure, Function, and Dynamics of Biomolecular Complexes - West Virginia University Department of Chemistry, January 2019

2018

  • E.H. Brookes, J. Pérez, P. Vachette and M. Rocco. Advances to the Ultrascan Solution Modeler (US-SOMO) SAS and HPLC-SAXS modules. XVII International Small Angle Scattering Conference - SAS2018 October 7-12, 2018, Traverse City, Michigan USA.
  • E.H. Brookes, J.E. Curtis, D. Fushman, S. Krueger, A. Savelyev. The GenApp Framework for SAS and Beyond. XVII International Small Angle Scattering Conference - SAS2018 October 7-12, 2018, Traverse City, Michigan USA. Poster
  • E.H. Brookes. PVP - P-Value Pair Map. XVII International Small Angle Scattering Conference - SAS2018 October 7-12, 2018, Traverse City, Michigan USA. Poster
  • J.E. Curtis, C. Jeonga, R. Franklin, K.J. Edler. Towards truly stealth nanodiscs. XVII International Small Angle Scattering Conference - SAS2018 October 7-12, 2018, Traverse City, Michigan USA. Poster
  • A.Y. Xu, M.M. Castellanos, K. Mattison, S. Krueger, J.E. Curtis. Physical Stability and Viscosity Behavior of NISTmAb Reference Material in Various Excipient Conditions. XVII International Small Angle Scattering Conference - SAS2018 October 7-12, 2018, Traverse City, Michigan USA. Poster
  • A. McClusky, S. Parker, K.J. Edler. pylj: an open-source Python library for teaching the interaction between molecular simulation and scattering. XVII International Small Angle Scattering Conference - SAS2018 October 7-12, 2018, Traverse City, Michigan USA. IUCr Journals Prize for the Best Student Lecture, SAS2018
  • A. McClusky, S. Parker, K. Edler. Using high-performance computing and molecular dynamics to rationalise micelle structure from small-angle scattering. XVII International Small Angle Scattering Conference - SAS2018 October 7-12, 2018, Traverse City, Michigan USA.
  • S.J. Perkins, A.J. Osborne, R. Nan, A. Miller, J.S. Bhatt, J. Gor. Different folded-back monomeric solution structures for complement factor H clarify distinct functions in the wilde-type TYR402 and disease-related HIS402 allotypes. XVII International Small Angle Scattering Conference - SAS2018 October 7-12, 2018, Traverse City, Michigan USA.
  • G.K. Hui, J. Gor, J. Lu, P.D. Sun, S.J. Perkins. Atomistic X-ray solution scattering structures of human IgG1 and IgG4 antibody-receptro complexes. XVII International Small Angle Scattering Conference - SAS2018 October 7, 2018, Traverse City, Michigan USA.
  • E. Brookes, M. Rocco, S. Krueger, J. Curtis. Tutorials on US-SOMO and SASSIE web presented at the BioSAS:Advanced Applications workshop at the XVII International Small Angle Scattering Conference - SAS2018 October 7-12, 2018, Traverse City, Michigan USA.
  • Savelyev, A, Brookes, E. Plotting Advancements to the GenApp Framework. Gateways 2018 September 25-27, 2018, University of Texas, Austin, TX USA.
  • N. Leung, E. Brookes, J. E. Curtis. JSSSE: An Extensible and Configurable Molecular Structure Editor for Scientific Gateways. Gateways 2018 September 25-27, 2018, University of Texas, Austin, TX USA. Poster
  • Y. Chen, A. Savelyev, E. Brookes, D. Fushman. ROTDIF-Web: A GenApp Generated Science Gateway for Comprehensive Analysis of Biomolecular NMR Relaxation Data. Gateways 2018 September 25-27, 2018, University of Texas, Austin, TX USA. Poster
  • J. Wereszczynski - Exploring the Relationship Between the Structure, Function, and Dynamics of Biomolecular Complexes - Illinois Institute of Technology Department of Physics, September 2018
  • A. McClusky, B. Morgan, S. Parker, K.J. Edler. Introducing programming to undergraduate chemists: and the tools we’ve developed to help them. PYCON UK, Cardiff, September 16, 2018.
  • J S Bhatt. Molecular dynamics combined with SANS. ‘Neutrons and Biology’ School of the French Neutron Society, September 16-19, 2018, Carqueiranne, France
  • Brookes, E.H. Definition File Generation of Science Gateways using GenApp, International Workshop on Science Gateways, IWSG18, 15 June 2018, Edinburgh, UK.
  • S.J.Perkins. Monte Carlo atomistic modelling of X-ray and neutron scattering data for human IgG1 and IgG4 antibodies reveals new insights on antibody solution structure and function. 3rd International Conference on Biosciences (ICB-2018) from 9-11th May, 2018, Science block, GC University Lahore Pakistan.
  • S.J.Perkins. Monte Carlo atomistic modelling of X-ray and neutron scattering data for human IgG1 and IgG4 antibodies reveals new insights on antibody solution structure and function. National Institute for Biotechnology & Genetic Engineering, Faisalabad, Pakistan. May 10, 2018
  • J. Wereszczynski - Exploring the Relationship Between the Structure, Function, and Dynamics of Biomolecular Complexes - Temple University Department of Physics, April 2018
  • S.J.Perkins. The CCP-SAS project on atomistic modelling of SAS data. Neutrons and Global Challenges II: Health and Healthcare. Institute of Physics, Feb 9, 2018. London, UK.
  • D.J. Scott. Neutron scattering with disordered proteins: soft matter techniques applied to hard biology. Neutrons and Global Challenges II: Health and Healthcare. Institute of Physics, Feb 9th 2018. London, UK.

2017

  • D.J. Scott. Intrinsic disorder in the KorB system. School of Vetinary and Medical Sciences, 15th Nov 2017. Nottingham, UK.
  • K. Edler. Polymer Effects on Formation of Polymer-Stabilized Lipid Nanodiscs. Nanoparticle Technologies for Membrane Protein Research, Jun 27, 2017. Leeds, UK.
  • E. Brookes & A. Savelyev. GenApp Integrated with OpenStack Supports Elastic Computing on Jetstream. Practice & Experience in Advanced Research Computing Conference, Jul 9-13 2017. New Orleans, USA.

2016

  • A. Savelyev & E. Brookes. GenApp: Extensible Tool for Rapid Generation of Web and Native GUI Applications. Gateways 2016 Conference, Nov 3, 2016. San Diego, California.
  • J. Chen. Towards Reliable Atomistic Simulation of Disordered Protein Ensembles. 252nd American Chemical Society Annual Meeting, Aug 21-25, 2016. Philadelphia, USA.
  • K. Lee, J. Chen. Towards a Balanced Implicit Solvent Force Field for Intrinsically Disordered Proteins. 252nd American Chemical Society Annual Meeting, Aug 21-25, 2016. Philadelphia, USA.
  • X. Liu, J. Chen. Coarse-grained model for multi-scale simulation enhanced sampling of intrinsically disordered protein conformations. 252nd American Chemical Society Annual Meeting, Aug 21-25, 2016. Philadelphia, USA.
  • E.Brookes, P. Vachette, J. Pérez, M. Rocco. Recent updates to the UltraScan SOlution MOdeler (US-SOMO) HPLC-SAXS data analysis module. ACA 2016, Jul 23, 2016. Denver, USA.
  • S. Krueger, C. Castañeda, J. Curtis, D. Fushman. Linkage-Specific Conformational Ensembles of Polyubiquitin Chains Revealed by NMR, SANS and Ensemble Structure Modeling. ACA 2016, Jul 23, 2016. Denver, USA.
  • S.C. Howell, E. Brookes, J. Curtis. Using Python to Create an Integrated Modular Framework for Atomistic Modeling of Molecular Structures. Scientific Computing with Python. Jul 11-17, 2016. Austin, USA. (See 09:11-14:03 mins)
  • J. Chen. Multi-scale modeling of IDP structure and interaction. 251st American Chemical Society National Meeting, Mar 13-17, 2016. San Diego, USA.
  • S. Perkins. CCP-SAS ? a community consortium for the atomistic modelling of scattering data: example applications. International Conference on Molecular Recognition. Feb 1, 2016. Zaragoza, Spain.

2015

  • K. Edler. Polymer stabilized phospholipid nanodiscs. In Symposium ?Self-assembled Biofunctional Nanomaterials?, Pacifichem, Dec 15 ? 20, 2015, Honolulu, USA.
  • K. W. Fung, R. Nan, M. Swann and S. J. Perkins. Dual polarization interferometry: characterisation of complement Factor H and C4b binding orientation to surfaces. Farfield and QCM-D User Meeting. Oct 26-28, 2015. Manchester University, UK.
  • J. Curtis. Neutron Scattering and Simulation for Structural Biology and Biotechnology. Oct 21, 2015. Kansas State University, USA.
  • J. Chen. Multi scale Simulations of IDP Structure and Interaction. 12th New England Structure Symposium, Oct 10, 2015. Storrs, USA.
  • E. Brookes, A. Kapoor, P. Patra, S. Marru, R. Singh, M. Pierce. GSoC 2015 student contributions to GenApp and Airavata. 10th Gateway Computing Environments Workshop, Sep 30, 2015. Boulder, USA.
  • J. Curtis. Software for Atomistic Modeling and Analysis of X-ray and Neutron Scattering Data. Sep 21, 2015. Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
  • W. Zhang, A. Heindel, D. Wright, J. Curtis, J. Chen. Advanced sampling and atomistic modeling for structural interpretation of small angle scattering. 16th International Conference on Small-Angle Scattering, Sep 13-18, 2015. Berlin, Germany.
  • J. Curtis. CCP-SAS - A community consortium for the atomistic modelling of scattering data. 16th International Conference on Small-Angle Scattering, Sep 16, 2015. Berlin, Germany.
  • S. Perkins. The asymmetric solution structures of native and patient monomeric human IgA1 reveal new insights on IgA nephropathy. 16th International Conference on Small-Angle Scattering, Sep 15, 2015. Berlin, Germany.
  • J. Curtis & D. Wright. Live demonstration of SASSIE-Web. 16th International Conference on Small-Angle Scattering, Sep 14, 2015. Berlin, Germany.
  • J. Chen. Towards Reliable Atomistic Simulations of Disordered Ensembles. CECAM Workshop on Intrinsically Disordered Proteins - Bringing together Physics, Computation and Biology, Aug 18-21, 2015. Zürich, Switzerland.
  • H. Zhang, J. Curtis, E. Brookes. Massively Parallel Computation for Small Angle Scattering. 65th Annual Meeting of American Crystallography Association, Jul 28, 2015. Philadelphia, USA.
  • S. Krueger. SANS Contrast Variation Experiments on Protein Complexes with Disordered Subunits. 65th Annual Meeting of American Crystallography Association, Jul 26, 2015. Philadelphia, USA.
  • J. Curtis, S. Perkins, P. Butler, S. King, J. Chen, H. Zhang, D. Wright, E. Brookes. CCP-SAS: A Community Consortium for the Atomistic Modelling of Scattering Data. 65th Annual Meeting of American Crystallography Association, Jul 26, 2015. Philadelphia, USA.
  • J. Curtis. SASSIE: A framework for multi-scale modeling of scattering data. EMBO Practical Course on Small angle neutron and X-ray scattering from proteins in solution, May 19, 2015. Grenoble, France.
  • E. Brookes. Gateways Application Generation with GenApp. XSEDE Weekly Gateways Seminar, May 1, 2015.
  • D. Wright, R. Nan, G.-K. Hui, J. Curtis, E. Brookes, S. Perkins. CCP-SAS - Novel approaches for the atomistic modelling of small angle scattering data in biology. 59th Biophysical Society Annual Meeting, Feb 7-11, 2015. Baltimore, USA.
  • K. Lee, J. Chen. Refining Multi-scale Enhanced Sampling for Simulating Disordered Protein Conformations. 59th Biophysical Society Annual Meeting, Feb 7-11, 2015. Baltimore, USA.
  • D. Wright, R. Nan, G.-K. Hui, J. Curtis, E. Brookes, S. Perkins. CCP-SAS - Novel approaches for the atomistic modelling of small angle scattering data in biology. CCP-Biosim Meeting. Jan 7-9, 2015. Leeds, UK.

2014

  • E. Brookes. An Open Extensible Application Generation Tool for Simple Rapid Deployment of Multi-Scale Scientific Codes. University of Texas at San Antonio, Computer Science Department talk. San Antonio, USA.
  • J. Chen. Orderly Chaos of Proteins. University of Kansas Medical Center, Biochemistry and Molecular Biology departmental seminar, Dec 19, 2014. Kansas City, USA.
  • E. H. Brookes, N. Anjum, J. E. Curtis, S. Marru, R. Singh, M. Pierce. GenApp module execution and airavata integration. 9th Gateway Computing Environments Workshop, SC14, Nov 16-21, 2014. New Orleans, USA.
  • P. Butler. CCP-SAS ? a new Collaborative Computational Project for the atomistic or coarse grained modelling of SANS and SAXS data. Joint PSB/COLLEGE 8 Seminar, Oct 16, 2014. Grenoble, France.
  • J. Chen. Multi-Scale Enhanced Sampling of Protein Structure and Interaction. Shanghai Jiao Tong University, Department of Physics seminar, Sept 22, 2014. Shanghai, China.
  • E. Rodriguez. A revised mechanism for the activation of complement C3 to C3b and a molecular explanation of the difference between their C3S and C3F polymorphic forms. XXV International Complement Workshop, Rio de Janeiro, Sep 14-18, 2014.
  • J. Chen. Multi-Scale Enhanced Sampling of Protein Structure and Interaction. Xiamen University, Department of Physics seminar, Sept 14, 2014. Xiamen, China.
  • S. J. Perkins, G.-K. Hui, L. Rayner. Atomistic modelling of SANS and SAXS data in applications to diverse antibody classes important in biotechnology and disease. Neutron Characterisation in Fundamental and Applied Biotechnology (NCFAB). Sep 3-5, 2014. Abingdon, UK.
  • J. Chen. Accelerate sampling in atomistic energy landscapes using coarse-grained models for implicit solvent optimization. 248th ACS National Meeting, Aug 10-14, 2014. San Francisco, USA.
  • E. Brookes. An Open Extensible Multi-Target Application Generation Tool for Simple Rapid Deployment of Multi-Scale Scientific Codes. XSEDE 2014 Annual Conference on Extreme Science and Engineering Discovery Environment, Jul 13-18,. 2014. Atlanta, USA.
  • S Perkins. Atomistic scattering modelling in CCP-SAS - its application to human IgG4. British Biophysical Society Biennial Meeting 2014, Jul 9-11, 2014. Warwick, UK.
  • R. Nan, C. M. Furze, D. W. Wright, R. Wallis, S. J. Perkins. The solution structures of MASP (mannose-binding lectin-associated serine protease) and MBL (mannose-binding lectin) provides insight on the activation of the lectin pathway of complement. British Biophysical Society Biennial Meeting 2014, Jul 9-11, 2014. Warwick, UK.
  • E. Brookes. Optimizing utilizable information from small angle solution scattering of biological macromolecules. British Biophysical Society Biennial Meeting 2014, Jul 9-11, 2014. Warwick, UK.
  • E. Brookes, M. Rocco. UltraScan-SOMO (US-SOMO): An Integrated Hydrodynamic Calculation and Small Angle Scattering Data Analysis Software Suite. 3rd S4SAS Workshop, Jul 7-9, 2014. Didcot, UK.
  • J. Chen. Accelerate sampling in atomistic energy landscapes using topology-based coarse-grained models. Telluride Workshop on Advances in Enhanced Sampling Algorithms, Jun 30 ? Jul 4, 2014. Telluride, USA.
  • S. Perkins. European Molecular Biophysics Facility Network Initiative. 5-6 June 2014. Institut Pasteur, Paris, France.
  • H. Zhang. Simulation of Neutron Data of Intrinsically Disordered Proteins and Nucleic Acids: Part II. ACNS 2014, Jun 1-5, 2014. Knoxville, USA.
  • J. E. Curtis. Introduction to Simulation Methods Applied to Modelling Neutron Scattering Structural Data. ACNS 2014, Jun 1-5, 2014. Knoxville, USA.
  • J. Perez, M. Rocco, E. Brookes. Bio SAS Data Analysis within US-SOMO. ACA 2014, May 24-28, 2014. Albuquerque, USA.
  • J. E. Curtis & H. Zhang. SASCALC – A fast and accurate small-angle scattering calculator for atomistic ensembles. ACA 2014, May 24-28, 2014. Albuquerque, USA.
  • P. Vachette, J. Perez, M. Rocco, E. Brookes. New developments in the UltraScan SOlution MOdeler (US-SOMO) HPLC-SAXS data analysis module. ACA 2014, May 24-28, 2014. Albuquerque, USA.
  • E. Brookes. Progress in Parsimonious Spatial Modelling of Biological SAS Experimental Data. ACA 2014, May 24-28, 2014. Albuquerque, USA.
  • P. Butler. CCP-SAS: A Collaborative Computational Project for Small Angle Scattering Modelling. SI2 PI workshop, Feb 24-25, 2014. Arlington VA.
  • S. Perkins, D. Wright, J. Curtis. CCP-SAS ? a new community consortium for the atomistic modelling of SANS and SAXS data. Neutrons in Biology and Biotechnology, February 19-21, 2014. Grenoble, France.