Test on-line:

The programs usage in Scientific publications 3D-Match
CYS_REC
GetAtoms
NNSSP
Pdisorder
PSSFinder
SSP
SSPAL

3D-Match

Drug target insights
2014, 8, 1. DOI: 10.4137/DTI.S13529

In Silico Molecular Characterization of Cysteine Protease YopT from Yersinia pestis by Homology Modeling and Binding Site Identification.

Hasan, M. A., Alauddin, S. M., Al Amin, M., Nur, S. M., Mannan, A.
Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Chittagong, Chittagong-4331, Bangladesh.

... regions. The selected model was further analyzed with verify 3D, 29 ERRAT 30 and 3D Match from Softberry (http://linux1.softberry.com/). ... plot. Verification was also done with verify 3D model, ERRAT, 3D match program from softberry. ...


Protein Science
Volume 19, Issue 3, pages 372–382, March 2010

Pyrroline-5-carboxylate synthase and proline biosynthesis: From osmotolerance to rare metabolic disease

Perez-Arellano, I., Carmona-Alvarez, F., Martinez, A. I., Rodriguez-Diaz, J. and Cervera, J
1. Molecular Recognition Laboratory. Centro de Investigacion Principe Felipe, Valencia, Spain 2. Centro de Investigacion Biomedica en Red de Enfermedades Raras (CIBERER-ISCIII), Valencia, Spain

... maritima (PDB ID 1O20) forms a tetramer made up of a dimer of dimers in which both the dimeric and the tetrameric contacts are extensive.35 These two 3D structures superim- pose with an RMSD of 1.8 A over 214 residues (pre- dicted by using 3D-Match by Softberry, Inc.) [Fig ... 


CYS_REC

Turkish Journal of Biology
2016, 40(3), p.623-633. .

Modeling of PrnD protein from Pseudomonas fluorescens RajNB11 and its comparative structural analysis with PrnD proteins expressed in Burkholderia and Serratia

SINGH, R. N., SINGH, R. P., SHARMA, A., & SAXENA, A. K.

... hydropathy (GRAVY) (Kyte and Doolittle, 1982). The sulfide bond pattern (SS) and linkages were predicted by the CYS_REC (http://linux1.softberry.com/ berry.phtml/topic) tool. PSIPRED v3.3 (http://bioinf. cs.ucl.ac.uk/psipred ...


Journal of Biotech Research [ISSN: 1944-3285]
2016, 7, 1-10.

Computational characterization and structure prediction of chitinase gene of beauveria bassiana using proteomic tools

Sood, S., Sandhu, S. S., Kumar, A. K., Gupta, A., Mukherjee, T. K.
1 Department of Biotechnology, Maharishi Markandeshwar University, Mullana , Ambala 133207, India. 2 Department of Biological Sciences, R. D. University, Jabalpur 482001, (MP) India.

... Disulphide linkages are important in functional characterization and bonds are predicted by the tool CYS_REC (http://sunI.softberry.com/berry.phtml?topic), which helps to identify the positions and total number of cysteines, and predicts the most probable "SS" bond pattern of ...


PloS one
2016, 11(1), e0145745. http://dx.doi.org/10.1371/journal.pone.0145745

Cloning and Expression of Phytase appA Gene from Shigella sp. CD2 in Pichia pastoris and Comparison of Properties with Recombinant Enzyme Expressed in E. coli.

Roy, M. P., Mazumdar, D., Dutta, S., Saha, S. P., Ghosh, S.
Department of Biotechnology, University of North Bengal, Siliguri, India

... The amino acid sequence encoded by the ORF was analyzed for the presence of signal peptide by SignalP 4.1 Server(http://www.cbs.dtu.dk/services/SignalP) [17] and for disulphide bond in the tertiary structure by using Softberry CYS_REC online services (www.softberry.com). ...


Applied biochemistry and biotechnology
2015, 176(3), 712-729. DOI: 10.1007/s12010-015-1606-2

1. Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University, Jeju Do, 690-756, Republic of Korea 2. Animal Genetic Resources Station, National Institute of Animal Science, Rural Development Administration, Namwon, Republic of Korea

Ghosh, M. et al.,
Department of Animal Biotechnology, Faculty of Biotechnology, Jeju National University

... The CYS_REC tool (www.?softberry.?com/?berry.?phtml??topic=?cys_?rec&? group=?programs&?subgroup=?propt) published by Softberry was used to predict the most probable SS bond pattern in the sequences [28]. ...


International Journal of Pharmaceutical Sciences and Research
2015, 6(4), 1727-1735. DOI: 10.13040/IJPSR.0975-8232.6(4).1727-35

COMPUTATIONAL MODELLING AND FUNCTIONAL CHARACTERIZATION OF HDAC-11

Samant, L. R., Sangar, V. C., Gulamaliwala, A., Chowdhary, A. S.
Systems Biomedicine Division 1, Department of Virology & Immunology 2, Haffkine Institute for Training, Research & Testing, Acharya Donde Marg, Parel, Mumbai - 400012. India.

... Functional characterization was computed using RaptorX, HMMTOP and SoftBerry Server's CYS_REC tool which predicted the secondary structure composition, presence of transmembrane proteins and the presence of cysteine residues respectively. Full Text. Keywords: ...


Asian Journal of Pharmaceutical & Clinical Research
Apr 2013 Supplement 2, Vol. 6, p265-268

SYNTHESIS AND MOLECULAR DOCKING STUDIES OF 2 CHOLROMETHYL-3-METHYL-1-PHENYL SULFONYL-1H-INDOLE COMPOUND

B., SARAVANAN; UPGADE, AKHILESH; BHASKAR, ANUSHA; V., MANIVANNAN

... The presence of SS bond and their bonding patterns were predicted by CYS_REC (16) and RASMOL server. CYS_REC (http://linux1.softberry.com/berry ... 23 283 16. CYS_REC.http://sun1. softberry.com/berry.phtml?topic=cys_rec &group=help &subgroup-propt. (27/10/2006) 17. ...


Structural Biology
Volume 2013 (2013), Article ID 370820, 10 pages http://dx.doi.org/10.1155/2013/370820

In Silico Characterization and Homology Modeling of a Cyanobacterial Phosphoenolpyruvate Carboxykinase Enzyme

Aubrey A. Smith and Amanda Caruso
Department of Biology, Montgomery College-Rockville Campus, 51 Mannakee Street, Rockville, MD 20850, USA

... disulfide patterns of each cyanobacterial PEPCK are tabulated in Table 3. The presence of disulfide bridges was analyzed using the CYS-REC tool which predicts the most probable bonding patterns between available cysteine residues (http://linux1.softberry.com/berry.phtml). ...


INT. J. BIOAUTOMATION,
2012, 16(4), 225-238 

In silico Characterization of Plant and Microbial Antifreeze Proteins

Md. Musharaf Hossain et al.,
Department of Genetic Engineering and Biotechnology Shahjalal University of Science and Technology Sylhet-3114, Bangladesh

... particular protein. The presence of SS bond and their bonding pairs were predicted by CYS_REC (http://linux1.softberry.com/berry phtml?topic) and “What If” server (identify SS bonds from 3D structure of a protein). The secondary ...


World Journal of Fish and Marine Sciences
5 (4): 426-429, 2013 DOI:10.5829/idosi.wjfms.2013.05.04.7427

Comparative in Silico Analysis of Mbl Homologues of Teleosts

Chirag Goel 1, Ashoktaru Barat 1, Veena Pande 2 and P.K. Sahoo 1
1 Molecular Genetics Laboratory, Directorate of Coldwater Fisheries Research (ICAR), Bhimtal-263136, Nainital, Uttarakhand, India 2 Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India

... test tube. There are certain dipeptides, the occurrence of structure (protein sequence data) by the tool CYS_REC which is significantly different in the unstable protein (http://sunI. softberry.com/ berry.phtml?topic). CYS_REC compared with those in the stable ones. This method ...


Bioinformation.
2013; 9(16): 802–807. DOI: 10.6026/97320630009802

in-silico characterization of b-(1, 3)-endoglucanase (ENGL1) from Aspergillus fumigatus by homology modeling and docking studies

Rizwan Ahmed, 1 Swatantra Kumar Jain, 2 and Praveen Kumar Shukla 1
1Medical Mycology lab, Division of Microbiology, CSIR-Central Drug Research Institute, Sitapur Road, Lucknow-226001, India 2Department of Biotechnology, Jamia Hamdard University, New Delhi, India

... Protein Topology prediction: Secondary structure of the protein ENGL1 from Aspergillus fumigatus was calculated with PSIPRED (http: //bioinf.cs.ucl.ac.uk/ psipred) and disulfide bonds were predicted by the Cys_REC tool (http://sunl.softberry.com/berry.phtml?topic). ...


Journal of PROTEINS AND PROTEOMICS
Vol 3, No 3 (2012)

IN SILICO CHARACTERIZATION OF BOVINE (BOS TAURUS) ANTIAPOPTOTIC PROTEINS

V G Vidhya, Akhilesh Upgade, Anusha Bhaskar, Dipanjana Deb
State

... RASMOL server. CYS_REC (http://linux1. softberry.com/berry.phtml) identified the position of a cysteine, total number of cystiene presented along with the most probable –SS- bond pairs in the protein sequences. The latter tool ...


Bioinformation
2013; 9(13): 680–684. DOI:10.6026/97320630009680

Insight from the structural molecular model of cytidylate kinase from Mycobacterium tuberculosis

Nitin Kumar Verma 1,2,* and Balwinder Singh 3
1Department of Bioscience, Shri Ram College, Muzaffarnagar 2Uttarakhand Technical University, Dehradun 3Department of Science, Ek Onkar Scholar Degree College, Shahbjnagar, Shahjahanpur

... The results are showing in Table 2 (see supplementary material). Functional characterization: CYC_REC (http://sunl.softberry.com/berry.phtml?topic) was used to locate “SS bond” between the pair of cystein residue, if present. ...


International Journal of Pharma & Bio Sciences
Jul-Sep2013, Vol. 4 Issue 3, pB-181-B-193. 13p.

IN SILICO CHARACTERIZATION OF HUMAN TYROSINASE USING COMPUTATIONAL TOOLS AND SERVERS

SEN GUPTA; PARTH SARTHI; BUDDHADEV MONDAL; BANDYOPADHYAY AMAL KUMAR

... Prot. Chem. 23 283 35. CYS_REC.http://sun1.softberry.com/berry.ph tml?topic= cys_rec&group=help&subgroup= propt. (27/10/2006) 36. Lambert C, Leonard N, De Bolle X and Depiereux E 2002 Bioinformatics 18 1250 37. Lovell. ...


INT.J. BIOAUTOMATION,
2012, 16(4), 225-238

In silico Characterization of Plant and Microbial Antifreeze Proteins

Hossain et al.,
Department of Genetic Engineering and Biotechnology Shahjalal University of Science and Technology Sylhet-3114, Bangladesh

... particular protein. The presence of SS bond and their bonding pairs were predicted by CYS_REC (http://linux1.softberry.com/berry phtml?topic) and “What If” server (identify SS bonds from 3D structure of a protein). The secondary ...


International Current Pharmaceutical Journal (ICPJ)
2012, Volume 1, Issue 2, pp 18-26 DOI

Fish antifreeze proteins: Computational analysis and physicochemical characterization

Md. Musharaf Hossain

.. Disulphide bonds are very essential in determining the functional linkage and the stability of a particular protein. The presence of SS bond and their bonding patterns were predicted by CYS_REC and What If server. CYS_REC (http://linux1.softberry.com/berry.phtml? ...


J Glob Infect Dis.
2012 Jan-Mar; 4(1): 43–54. doi: 10.4103/0974-777X.93761

Analyzing a Potential Drug Target N-Myristoyltransferase of Plasmodium falciparum Through In Silico Approaches

Amit Kumar Banerjee, Neelima Arora, and USN Murty
Bioinformatics Group, Biology Division, Indian Institute of Chemical Technology, Tarnaka, Uppal Road, Hyderabad, Andhra Pradesh, India

... of 0.05 and number of possible pseudomotifs predicted was kept 3. CYSREC (http://linux1.softberry.com/) was used to predict the cysteine pairing pattern. As some proteins are known to contain several unstructured or disordered ...


PLoS ONE
7(12): e50900. doi:10.1371/journal.pone.0050900

Molecular Cloning and Characterization of Novel Morus alba Germin-Like Protein Gene Which Encodes for a Silkworm Gut Digestion-Resistant Antimicrobial Protein

Patnaik et al.,
Division of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea

... and NetPhosK 1.0 server respectively [36]–[39]. Disulfide bonds were predicted by the Cys_REC tool (version 2.0) from Softberry (http://linux1.softberry.com/berry. phtml/). The superfamily and the conserved domains including ...


Bioinformation
8(17): 807-811 (2012)

Homology Modeling and Functional Characterization of PR-1a Protein of Hordeum vulgare subsp. Vulgare

Vahid Aslanzadeh 1 * & Mostafa Ghaderian 2, 3
1Department of Biotechnology, Research Institute of Physiology and Biotechnology, University of Zanjan, Zanjan, Iran; 2Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia;

... Protein was further subjected to CYS_REC program(http://linux1.softberry.com/berry. phtml?topic=cys_rec&gro up=programs&subgroup=propt) for locating SS-bonding states of cysteines and disulphide bridges in proteins, if present. ...


J Proteomics Bioinform
2012, 5:9 http://dx.doi.org/10.4172/jpb.1000238

Homology Modeling and Structural Analysis of NHX Antiporter of Leptochloa fusca (L.)

Panahi et al.,
1Department of Biotechnology and Plant Breeding, Ferdowsi University of Mashhad, Mashhad, Iran 2Department of Biotechnology, University of Isfahan, Iran

...CYS_REC (http://sunl.softberry.com/ berry.phtml?topic) was used to locate “SS bond” between the pair of cysteinee residues, if present. ...


IJPSR,
2012; Vol. 3(7): 2050-2056

IN-SILICO ANALYSIS AND HOMOLOGY MODELING OF TARGET PROTEINS FOR CLOSTRIDIUM BOTULINUM

Chirag Prajapati*1 and Chintan Bhagat 2
Department of Computer Science (Bioinformatics) 1, Department of Biotechnology 2, Veer Narmad South Gujarat University, Surat, Gujarat, India

... Disulphide bonds are important in determining functional linkages. Table 4 shows prediction of “SS” bonds using primary structure (protein sequence data) by tool CYS_REC http://linux1.softberry.com/berry.phtml?topic=cys_rec &group=programs&subgroup=propt. ...


Bioinformation
2011; 6(8): 315–319. PMCID: PMC3134781

Structure prediction and functional characterization of secondary metabolite proteins of Ocimum

Roy et al.,
Biotechnology Division, Central Institute of Medicinal and Aromatic Plants, (Council of Scientific and Industrial Research), Kukrail Picnik Spot Road, P.O. CIMAP, Lucknow - 226015, India

... protparam.html). The results are shown in (see Table 4). Functional characterization. CYS_REC (http://sunl.softberry.com/berry.phtml? topic) was used to locate “SS bond” between the pair of cystein residues, if present. The tool ...


Current Research Journal of Biological Sciences
3(1): 35-41, 2011 DOI:

Physiochemical, Functional and Structural Characterization of Wheat Germin Using In silico Methods

Vinita Hooda
Department of Botany, M.D. University, Rohtak -124001, Haryana, India

... For functional characterization disulfide bonds were predicted by the Cys_REC tool from softberry, secondary structures were calculated with SOPMA (Self Optimized Prediction Method with Alignment) (Geourjon and Deleage, 1995). ...


Journal of Applied Sciences in Environmental Sanitation
Volume 6, Number 3: 357-366, September, 2011

Structural Analysis and 3D-Modelling of Fur Protein from Bradyrhizobium japonicum

Singh et al.,
1National Bureau of Agriculturally Important Microorganisms (ICAR), Kushmaur, Kaithauli, Mau Nath Bhanjan, Uttar Pradesh-275101, India. 2Department of Botany and Microbiology, Gurukul Kangri University, Haridwar, Uttrakhand-249404, India.

... The sulphide (SS) bond pattern is predicted by using the tool CYS_REC (http://linux1.softberry.com/berry.phtml?topic), has shown that fur protein has three cysteine residues at position 19, 53 and 141, and have no SS bonding. ...


POJ
4(7):354-363 (2011)

In silico approaches in comparative genomics, structure prediction and functional characterization of secondary metabolite proteins of Mentha sp

Roy et al.,
1Biotechnology Division, Central Institute of Medicinal and Aromatic Plants, Council of Scientific and Industrial Research, Lucknow - 226015, India 2 IIDS Center of Bioinformatics, Nehru Science Center, University of Allahabad, Allahabad - 211001, India

... Disulphide bridges were find using Cys_REC tool from softberry (Table 7). Domain and fold recognition ... Functional characterization of disulfide bonds present in secondary metabolite proteins of Mentha species were done by Cys_REC tool from Softberry. Page 9. 362 ...


Journal of Applied Sciences in Environmental Sanitation
2011, 6 (4): 485-494.

Homology Modeling and Sequence Analysis of a Highly Thermostable Endo-(1,4)-Beta-Mannase from the Marine Bacterium Rhodothermus Marinus.

ZRaghvendra Pratap Singh, Alok R. Rai, Kunal Roychoudhury and R.C. Dubey .
1Department of Botany and Microbiology, Gurukul Kangri University, Haridwar, Uttrakhand-249404, India 2Department of Microbiology, Seth Kesarimal Porwal College, Kamptee Maharashtra 441002, India

... The sulphide (SS) bond pattern is predicted by employing the tool CYS_REC (http://linux1.softberry.com/berry.phtml?topic), has shown that 1,4-?-D-mannanase protein has three cysteines residues at position 255,265 have no SS bonding. ...


J Proteomics Bioinform
2010 Volume:3 Issue:5 pp. 148-154 doi:10.4172/jpb.1000134

In silico Analysis and Homology Modelling of Antioxidant Proteins of Spinach

Archna Sahay ; Madhvi Shakya
1 Department of Bioinformatics, MANIT, Bhopal-462051 M.P., India 2 Department of Mathematics, MANIT, Bhopal-462051, M.P., India

... Journal of Proteomics & Bioinformatics - Open Access www.omicsonline.com CYS_REC (http://sunI.softberry.com/berry.phtml?topic). CYS_REC identifies the position of cysteins, total number of cysteins present and pattern, if present, of pairs in the protein sequence. ... 


Asian J. Exp. Sci.,
Vol. 22, No. 3, 2008; 265-274

In silico Characterization of Silk Fibroin Protein using Computational Tools and Servers

K.V. Ashokan and M.M. Pillai
Department of Biological Science, P.V.P College, K. Mahnakl, Sangli - 416405 (Maharashtra); India. Department of Biotechnology, KIT’s College of Engineering, Gokul Shirgaon, Kolhapur (Maharashtra); India.

... using CLC free workbench tool Page 4. 268 CYS_REC (http://sunI.softberry. com/ berry.phtml?topic). CYS_REC identifies the position of ...


J. Chem. Sci.,
Vol. 119, No. 5, September 2007, pp. 571–579.

In silico characterization of antifreeze proteins using computational tools and servers

K SIVAKUMAR, S BALAJI and GANGARADHAKRISHNAN
1Department of Chemistry, Sri Chandrasekharendra Saraswathi Viswa Maha Vidyalaya (Deemed University), Enathur, Kanchipuram 631 561 2EXCEL and Polymer Science Labs, Central Leather Research Institute, Adyar, Chennai 600 020

... CYS_REC identifies the positions of cysteines, total number of cysteines present and predicts the most probable SS bond pattern of pairs in the protein sequence. ...


GetAtoms

Cambridge University Press
2006

Essential Bioinformatics

J Xiong

... 9. Perform comprehensive homology modeling using the GetAtoms server (www.softberry. com/berry.phtml?topic=getatoms&group=programs& subgroup=propt). 10. ...


NNSSP

Plant Physiology
132:1391-1404 (2003)

Interacting Transcription Factors from the Three-Amino Acid Loop Extension Superclass Regulate Tuber Formation

Hao Chen, Faye M. Rosin, Salome Prat and David J. Hannapel
Interdepartmental Plant Physiology Major (H.C., D.J.H.) and Molecular, Cellular, and Developmental Biology Major (F.M.R., D.J.H.), Department of Horticulture, Iowa State University, Ames, Iowa 50011–1100; and Department of Plant Molecular Genetics, National Center of Biotechnology, Consejo Superior de Investigaciones Cientificas, Cantoblanco Campus University of Madrid, Madrid, Spain (S.P.)

... of the sequence structure was derived by using three software programs for amino acid sequence analysis: sspal, ssp, and nnssp (http://www.softberry.com/berry ...


Pdisorder

BMC Bioinformatics
2012, 13:153 doi:10.1186/1471-2105-13-153

Molecular evolution of dihydrouridine synthases

Joanna M Kasprzak 2, Anna Czerwoniec 2 and Janusz M Bujnicki 1,2
1 Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL-02-109, Warsaw, Poland 2 Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614, Poznan, Poland

... residues were made using MetaDisorder (http://iimcb.genesilico.pl/metadisorder/ webcite; [40], a meta-method which combines the predictions of the following primary methods: DisEMBL [41], DISPROT(VSL2) [42], GlobPlot [43], IUPred [44], PDISORDER (SoftBerry, http://linux1 ...


Molecular Genetics and Genomics
January 2012, Volume 287, Issue 1, pp 39-54

Molecular characterization and functional analysis by heterologous expression in E. coli under diverse abiotic stresses for OsLEA5, the atypical hydrophobic LEA protein from Oryza sativa L.

Shuai He et al.,
1. Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, China

... Secondary structure predictions were run with the DSSP, PSIPRED (http:// www.ibi.vu.nl/ programs) (Jones 1999; Kabsch and Sander 1983), PDISORDER (http://linux1.softberry.com), and DisEMBL (http://dis.embl.de/) programs (Linding et al. 2003). ...


Applied Biochemistry and Biotechnology
January 2012, Volume 166, Issue 1, pp 222-233 10.1007/s12010-011-9418-5

Molecular Analysis of OsLEA4 and Its Contributions to Improve E. coli Viability

Tingzhang Hu et al.,
1. Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, People’s Republic of China 2. School of Life Science and Engineering, Chongqing Three Gorges University, Chongqing, 404100, People’s Republic of China

... InterProScan/). Secondary structure predictions were run with the DSSP, PSIPRED (http://www.ibi.vu.nl/programs) [20, 21], PDISORDER (http://linux1.softberry.com), and DisEMBL (http://dis.embl.de/) programs [22]. Analysis ...


The EMBO Journal
2007, 26, 5071-5082, doi:10.1038/sj.emboj.7601916
A conserved function for a Caenorhabditis elegans Com1/Sae2/CtIP protein homolog in meiotic recombination

A. Penkner et al.,
1 Department of Chromosome Biology and Max F. Perutz Laboratories, Center for Molecular Biology, University of Vienna, Vienna, Austria 2 Developmental Genetics, TU Braunschweig, Germany 3 Bioinformatics Group, Research Institute of Molecular Pathology, Vienna, Austria


... They are mostly disordered and low-complex (Pdisorder; www.softberry.com) except for the C-terminal 70-100 aa corresponding to the region of highest sequence ...


BMC Bioinformatics
2005, 6:22 doi:10.1186/1471-2105-6-22

Research article Open Access
Proteins with two SUMO-like domains in chromatin-associated complexes: The RENi (Rad60-Esc2-NIP45) family

Maria Novatchkova*1, Andreas Bachmair3, Birgit Eisenhaber2 and Frank Eisenhaber2
Address: 1Gregor Mendel-Institut GMI, Austrian Academy of Sciences, Vienna Biocenter, A-1030 Vienna, Austria, 2Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, A-1030 Vienna, Austria and 3Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, D-50829 Cologne, Germany


...Initial analysis of its sequence complexity shows that the disordered N-terminal half of the protein is followed by a likely globular segment (predicted using Pdisorder by Softberry, Inc)...


PSSFinder

Frontiers in plant science
2014, 5: 26. DOI:10.3389/fpls.2014.00026

Plant 4/1 protein: potential player in intracellular, cell-to-cell and long-distance signaling

Morozov S. Y. et al.,
1 A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia 2 Department of Virology, Faculty of Biology, Moscow State University, Moscow, Russia

... PHYSICO-CHEMICAL PROPERTIES OF 4/1 PROTEIN. The Nt-4/1 protein is predicted by PSSFinder (Soli et al., 2009) (http://linux1.softberry.com/berry.phtml) to form six long alpha-helices and two short beta-sheet structures. ...


Australian Journal of Grape and Wine Research
Volume 19, Issue 2, pages 193–207, June 2013 DOI:10.1111/ajgw.12029

Polymorphisms in VvPel associate with variation in berry texture and bunch size in the grapevine

Vargas, A.M., Fajardo, C., Borrego, J., De Andres, M.T. and Ibanez, J.
1Instituto Madrileno de Investigacion y Desarrollo Rural, Agrario y Alimentario (IMIDRA), Alcala de Henares, Madrid, Spain 2Instituto de Ciencias de la Vid y del Vino (CSIC, Gobierno de La Rioja, Universidad de La Rioja), Complejo Cientifico Tecnologico, Logrono, Spain

... Prediction of secondary structure. The amino acid sequence for each haplotype was obtained, and secondary structure was predicted by means of the software PSSFinder, both implemented in Softberry, Inc. (NY, USA; http://linux1.softberry.com/berry.phtml). ...


Biochimie
Volume 95, Issue 7, July 2013, Pages 1360–1370 DOI:10.1016/j.biochi.2013.02.015

Subcellular localization and self-interaction of plant-specific Nt-4/1 protein

Solovyev A.G. et al.,
a A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Chochlova Str. 1, 119992 Moscow, Russia b M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Str., Moscow 117997, Russia

... 2) [6]. Predictions of the protein secondary structure carried out for Nt-4/1-CC-II using SSP and PSSFinder prediction methods available at the SoftBerry website (http://linux1.softberry.com/berry. phtml) revealed that the Pro residues introduced in Nt-4/1-CC-II precluded formation ...


Biochimie
Volume 93, Issue 10, October 2011, Pages 1770–1778 DOI: 10.1016/j.biochi.2011.06.018

Orthologues of a plant-specific At-4/1 gene in the genus Nicotiana and the structural properties of bacterially expressed 4/1 protein

Makarova et al.,
a Department of Virology, Biological Faculty, Moscow State University, Moscow 119992, Russia b M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklaya Str., Moscow 117997, Russia

... For computer-assisted secondary structure prediction, the PSSFinder server (http://linux1.softberry. com/berry.phtml) [20], the PCOIL server (http://toolkit.tuebingen.mpg.de/pcoils) [21] and [22] and the MARCOIL server (http://www.isrec.isb-sib.ch/webmarcoil/webmarcoilC1.html ...


BMC Pharmacology
2009, 9:4doi:10.1186/1471-2210-9-4

Bioinformatics’ characterizations and prediction of K+ and Na+ ion channels effector toxins

Rima Soli 1, a, Belhassen Kaabi 1, a, *, Mourad Barhoumi 1, Mohamed El-Ayeb2 , and Najet Srairi-Abid 2
1) Laboratory of Epidemiology and Ecology of Parasites, Institut Pasteur de Tunis, Tunis, Tunisia. (2) Laboratory of Venom and Toxins, Institut Pasteur de Tunis, Tunis, Tunisia

... The 2D structure of all the sequences (training and test datasets) was determined based on the program PHD [36-38] using neural network approach, and the Softberry's software PSSfinder [39], which uses Markov chains probabilistic model. Phylogenetic analysis ...


BMC Molecular Biology
2008, 9:88 doi:10.1186/1471-2199-9-88

Computational modeling and in silico analysis of differential regulation of myo-inositol catabolic enzymes in Cryptococcus neoformans

Emalee A Mackenzie and Lisa S Klig
1Life Sciences Department, Irvine Valley College, Irvine, CA, USA and 2Department of Biological Sciences, California State University, Long Beach, CA, USA

... 35. PSSFinder [http://www.softberry.ru/berry.phtml?topic=pps&group=programs&subgroup =propt] 36. SAM_T02 [http://www.softberry.com/all.htm] 37. ...


SSPAL

Plant Physiology
132:1391-1404 (2003)

Interacting Transcription Factors from the Three-Amino Acid Loop Extension Superclass Regulate Tuber Formation

Hao Chen, Faye M. Rosin, Salome Prat and David J. Hannapel
Interdepartmental Plant Physiology Major (H.C., D.J.H.) and Molecular, Cellular, and Developmental Biology Major (F.M.R., D.J.H.), Department of Horticulture, Iowa State University, Ames, Iowa 50011–1100; and Department of Plant Molecular Genetics, National Center of Biotechnology, Consejo Superior de Investigaciones Cientificas, Cantoblanco Campus University of Madrid, Madrid, Spain (S.P.)

... of the sequence structure was derived by using three software programs for amino acid sequence analysis: sspal, ssp, and nnssp (http://www.softberry.com/berry ...


SSP

Molecular Plant Pathology
Volume 9 Issue 4 Page 511-523, July 2008

Natural variation reveals key amino acids in a downy mildew effector that alters recognition specificity by an Arabidopsis resistance gene

REBECCA L. ALLEN et al.,
Warwick HRI, Warwick University, Wellesbourne, Warwick CV35 9EF, UK Department of Evolutionary Biology, University of Munich, Gro?haderner Str. 2, 82152 Planegg-Martinsried, Germany

... html). Prediction of alpha helix was by the SSP program (http://softberry. com/berry.phtml?topic=sspgroup=programssubgroup=propt). ...


Plant Physiology
132:1391-1404 (2003)

Interacting Transcription Factors from the Three-Amino Acid Loop Extension Superclass Regulate Tuber Formation

Hao Chen, Faye M. Rosin, Salome Prat and David J. Hannapel
Interdepartmental Plant Physiology Major (H.C., D.J.H.) and Molecular, Cellular, and Developmental Biology Major (F.M.R., D.J.H.), Department of Horticulture, Iowa State University, Ames, Iowa 50011–1100; and Department of Plant Molecular Genetics, National Center of Biotechnology, Consejo Superior de Investigaciones Cientificas, Cantoblanco Campus University of Madrid, Madrid, Spain (S.P.)

... of the sequence structure was derived by using three software programs for amino acid sequence analysis: sspal, ssp, and nnssp (http://www.softberry.com/berry ...



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