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1

Processing and analysis of CASP3 protein structure predictions

Adam Zemla, Česlovas Venclovas, John Moult, Krzysztof Fidelis

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 316 KB

english, 1999

2

Critical assessment of methods of protein structure prediction (CASP)-round V

John Moult, Krzysztof Fidelis, Adam Zemla, Tim Hubbard

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 69 KB

english, 2003

3

Numerical criteria for the evaluation of ab initio predictions of protein structure

Zemla, Adam, Venclovas, Česlovas, Reinhardt, Astrid, Fidelis, Krzysztof, Hubbard, Tim J.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 731 KB

english, 1997

4

Criteria for evaluating protein structures derived from comparative modeling

Česlovas Venclovas, Adam Zemla, Krzysztof Fidelis, John Moult

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1997

Language:

english

File:

PDF, 357 KB

english, 1997

5

Some measures of comparative performance in the three CASPs

Česlovas Venclovas, Adam Zemla, Krzysztof Fidelis, John Moult

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 320 KB

english, 1999

6

A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment

Adam Zemla, Česlovas Venclovas, Krzysztof Fidelis, Burkhard Rost

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

1999

Language:

english

File:

PDF, 100 KB

english, 1999

7

Amino acid and structural variability of Yersinia pestis LcrV protein

Andrey P. Anisimov, Svetlana V. Dentovskaya, Evgeniy A. Panfertsev, Tat’yana E. Svetoch, Pavel Kh. Kopylov, Brent W. Segelke, Adam Zemla, Maxim V. Telepnev, Vladimir L. Motin

Journal:

Infection, Genetics and Evolution

Year:

2010

Language:

english

File:

PDF, 446 KB

english, 2010

8

Comparison of performance in successive CASP experiments

Česlovas Venclovas, Adam Zemla, Krzysztof Fidelis, John Moult

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 2.80 MB

english, 2001

9

Critical assessment of methods of protein structure prediction (CASP): Round IV

John Moult, Krzysztof Fidelis, Adam Zemla, Tim Hubbard

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 66 KB

english, 2001

10

Processing and evaluation of predictions in CASP4

Adam Zemla, Česlovas Venclovas, John Moult, Krzysztof Fidelis

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2001

Language:

english

File:

PDF, 3.68 MB

english, 2001

11

Assessment of progress over the CASP experiments

C̆eslovas Venclovas, Adam Zemla, Krzysztof Fidelis, John Moult

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2003

Language:

english

File:

PDF, 993 KB

english, 2003

12

The other 90% of the protein: Assessment beyond the Cαs for CASP8 template-based and high-accuracy models

Daniel A. Keedy, Christopher J. Williams, Jeffrey J. Headd, W. Bryan Arendall III, Vincent B. Chen, Gary J. Kapral, Robert A. Gillespie, Jeremy N. Block, Adam Zemla, David C. Richardson, Jane S. Richa

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2009

Language:

english

File:

PDF, 1.45 MB

english, 2009

13

The Significance of Performance Ranking in CASP—Response to Marti-Renom et al.

John Moult, Krzysztof Fidelis, Adam Zemla, Tim Hubbard, Anna Tramontano

Journal:

Year:

2002

Language:

english

File:

PDF, 31 KB

english, 2002

14

StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase

Adam T Zemla, Dorothy M Lang, Tanya Kostova, Raul Andino, Carol L Ecale Zhou

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 2.67 MB

english, 2011

15

A study of quality measures for protein threading models

Susana Cristobal, Adam Zemla, Daniel Fischer, Leszek Rychlewski, Arne Elofsson

Journal:

BMC Bioinformatics

Year:

2001

Language:

english

File:

PDF, 625 KB

english, 2001

16

MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization

L Ecale Carol Zhou, Marisa W Lam, Jason R Smith, Adam T Zemla, Matthew D Dyer, Thomas A Kuczmarski, Elizabeth A Vitalis, Thomas R Slezak

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 314 KB

english, 2006

17

Computational analysis of pathogen-borne metallo β-lactamases reveals discriminating structural features between B1 types

Eithon Cadag, Elizabeth Vitalis, Kristin P Lennox, Carol L Ecale Zhou, Adam T Zemla

Journal:

BMC Research Notes

Year:

2012

Language:

english

File:

PDF, 1.18 MB

english, 2012

18

Antibody Elbow Angles are Influenced by their Light Chain Class

Robyn L. Stanfield, Adam Zemla, Ian A. Wilson, Bernhard Rupp

Journal:

Journal of Molecular Biology

Year:

2006

Language:

english

File:

PDF, 700 KB

english, 2006

19

Practical applications of structural genomics technologies for mutagen research

Adam Zemla, Brent W. Segelke

Journal:

Mutation Research/Genetic Toxicology and Environmental Mutagenesis

Year:

2011

Language:

english

File:

PDF, 352 KB

english, 2011

20

On the Fundamental Solutions for the Difference Helmholtz Operator

Journal:

SIAM Journal on Numerical Analysis

Year:

1995

Language:

english

File:

PDF, 924 KB

english, 1995

21

A strain of Yersinia pestis with a mutator phenotype from the Republic of Georgia

Rajanna, Chythanya, Ouellette, Gary, Rashid, Mohammed, Zemla, Adam, Karavis, Mark, Zhou, Carol, Revazishvili, Tamara, Redmond, Brady, McNew, Lauren, Bakanidze, Lela, Imnadze, Paata, Rivers, Bryan, Sko

Journal:

FEMS Microbiology Letters

Year:

2013

Language:

english

File:

PDF, 674 KB

english, 2013

22

On the Fundamental Solutions for the Difference Helmholtz Operator

Journal:

SIAM Journal on Numerical Analysis

Year:

1995

Language:

english

File:

PDF, 785 KB

english, 1995

23

Dimerization of cobalt-substituted Keggin phosphotungstate, [PW 11 O 39 Co(X)] 5− , in nonpolar solvents

Dannenhoffer, Adam, Baker, Jerry, Pantano, Nicholas, Stachowski, Jessica, Zemla, Derek, Swanson, William, Zurek, Eva, Szczepankiewicz, Steven, Kozik, Mariusz

Journal:

Journal of Coordination Chemistry

Year:

2014

Language:

english

File:

PDF, 501 KB

english, 2014

24

SpaK/SpaR Two-component System Characterized by a Structure-driven Domain-fusion Method and in Vitro Phosphorylation Studies

Chakicherla, Anu, Ecale Zhou, Carol L., Dang, Martha Ligon, Rodriguez, Virginia, Hansen, J. Norman, Zemla, Adam, Panchenko, Anna R.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 796 KB

english, 2009

25

A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes

Yelton, Alexis P., Thomas, Brian C., Simmons, Sheri L., Wilmes, Paul, Zemla, Adam, Thelen, Michael P., Justice, Nicholas, Banfield, Jillian F., Eisen, Jonathan A.

Journal:

PLoS Computational Biology

Year:

2011

Language:

english

File:

PDF, 1.04 MB

english, 2011

26

On the role of the degradation rates for the dominance of the fittest in Eigen's quasispecies model

Kostova, Tanya, Zhou, Carol, Zemla, Adam

Journal:

Journal of Biological Dynamics

Year:

2011

Language:

english

File:

PDF, 247 KB

english, 2011

27

The Sorting Receptor SorCS1 Regulates Trafficking of Neurexin and AMPA Receptors

Savas, Jeffrey N., Ribeiro, Luís F., Wierda, Keimpe D., Wright, Rebecca, DeNardo-Wilke, Laura A., Rice, Heather C., Chamma, Ingrid, Wang, Yi-Zhi, Zemla, Roland, Lavallée-Adam, Mathieu, Vennekens, Kris

Journal:

Year:

2015

Language:

english

File:

PDF, 5.36 MB

english, 2015

28

Identification of a Thermo-Regulated Glutamine-Binding Protein from Yersinia pestis

Cosman, Monique, Pesavento, Joseph, Zemla, Adam, Beernink, Peter, Balhorn, Rod, Barsky, Daniel

Journal:

Protein & Peptide Letters

Year:

2008

Language:

english

File:

PDF, 608 KB

english, 2008

29

Sendai virus intra-host population dynamics and host immunocompetence influence viral virulence during in vivo passage

Peña, José, Chen-Harris, Haiyin, Allen, Jonathan E., Hwang, Mona, Elsheikh, Maher, Mabery, Shalini, Bielefeldt-Ohmann, Helle, Zemla, Adam T., Bowen, Richard A., Borucki, Monica K.

Journal:

Virus Evolution

Year:

2016

Language:

english

File:

PDF, 1.76 MB

english, 2016

30

Light Regimes Shape Utilization of Extracellular Organic C and N in a Cyanobacterial Biofilm

Stuart, Rhona K., Mayali, Xavier, Boaro, Amy A., Zemla, Adam, Everroad, R. Craig, Nilson, Daniel, Weber, Peter K., Lipton, Mary, Bebout, Brad M., Pett-Ridge, Jennifer, Thelen, Michael P.

Journal:

Year:

2016

Language:

english

File:

PDF, 1.72 MB

english, 2016

31

Missing the trees for the forest: A construal level account of the illusion of explanatory depth.

Alter, Adam L., Oppenheimer, Daniel M., Zemla, Jeffrey C.

Journal:

Journal of Personality and Social Psychology

Year:

2010

Language:

english

File:

PDF, 249 KB

english, 2010

32

Microbial mercury methylation in Antarctic sea ice

Gionfriddo, Caitlin M., Tate, Michael T., Wick, Ryan R., Schultz, Mark B., Zemla, Adam, Thelen, Michael P., Schofield, Robyn, Krabbenhoft, David P., Holt, Kathryn E., Moreau, John W.

Journal:

Nature Microbiology

Year:

2016

Language:

english

File:

PDF, 1.97 MB

english, 2016

33

Complete genome sequence ofPseudomonas stutzeristrain RCH2 isolated from a Hexavalent Chromium [Cr(VI)] contaminated site

Chakraborty, Romy, Woo, Hannah, Dehal, Paramvir, Walker, Robert, Zemla, Marcin, Auer, Manfred, Goodwin, Lynne A., Kazakov, Alexey, Novichkov, Pavel, Arkin, Adam P., Hazen, Terry C.

Journal:

Standards in Genomic Sciences

Year:

2017

Language:

english

File:

PDF, 2.16 MB

english, 2017

34

Complete genome sequence of the chromate-reducing bacteriumThermoanaerobacter thermohydrosulfuricusstrain BSB-33

Pamela Bhattacharya,Adam Barnebey,Marcin Zemla…

Journal:

Standards in Genomic Sciences

Year:

2015

Language:

english

File:

PDF, 2.17 MB

english, 2015

35

Rapid Countermeasure Discovery against Francisella tularensis Based on a Metabolic Network Reconstruction

Chaudhury, Sidhartha, Abdulhameed, Mohamed Diwan M., Singh, Narender, Tawa, Gregory J., D’haeseleer, Patrik M., Zemla, Adam T., Navid, Ali, Zhou, Carol E., Franklin, Matthew C., Cheung, Jonah, Rudolph

Journal:

Year:

2013

Language:

english

File:

PDF, 617 KB

english, 2013

36

Structural Re-Alignment in an Immunogenic Surface Region of Ricin a Chain

Zemla, Adam T., Zhou, Carol L. Ecale

Journal:

Bioinformatics and Biology Insights

Year:

2008

Language:

english

File:

PDF, 570 KB

english, 2008

37

Multiscale analysis for patterns of Zika virus genotype emergence, spread, and consequence

Borucki, Monica K., Collette, Nicole M., Coffey, Lark L., Van Rompay, Koen K. A., Hwang, Mona H., Thissen, James B., Allen, Jonathan E., Zemla, Adam T., Khudyakov, Yury E

Journal:

Year:

2019

File:

PDF, 2.71 MB

2019

38

Single Amino Acid Mutations Affect Zika Virus Replication In Vitro and Virulence In Vivo

Collette, Nicole M., Lao, Victoria H. I., Weilhammer, Dina R., Zingg, Barbara, Cohen, Shoshana D., Hwang, Mona, Coffey, Lark L., Grady, Sarah L., Zemla, Adam T., Borucki, Monica K.

Journal:

Year:

2020

File:

PDF, 2.72 MB

2020

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