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Overview page. Subjects: Computing.

When a computer or a user is directly connected into a network and is capable of interacting with it, for example by querying the contents of a database.

See overview in Oxford Index

Interactive construction of residue-based diagrams of proteins: the RbDe web service

K. Konvicka, F. Campagne and H. Weinstein.

in Protein Engineering, Design and Selection

June 2000; p ublished online June 2000 .

Journal Article. Subjects: Proteins. 946 words.

We announce the Residue-based Diagram Editor (RbDe) web service that allows online construction of residue-based diagrams and the creation of stored diagram libraries. The service has been...

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AUTO-MUTE: web-based tools for predicting stability changes in proteins due to single amino acid replacements

Majid Masso and Iosif I. Vaisman.

in Protein Engineering, Design and Selection

August 2010; p ublished online June 2010 .

Journal Article. Subjects: Proteins. 3366 words.

Utilizing cutting-edge supervised classification and regression algorithms, three web-based tools have been developed for predicting stability changes upon single residue substitutions in...

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Amino acid quantitative structure property relationship database: a web-based platform for quantitative investigations of amino acids

Yi Lu, Blazej Bulka, Marie desJardins and Stephen J. Freeland.

in Protein Engineering, Design and Selection

July 2007; p ublished online June 2007 .

Journal Article. Subjects: Proteins. 3133 words.

Here, we present the AA-QSPR Db (Amino Acid Quantitative Structure Property Relationship Database): a novel, freely available web-resource of data pertaining to amino acids, both engineered...

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WAM: an improved algorithm for modelling antibodies on the WEB

Nicholas R.J. Whitelegg and Anthony R. Rees.

in Protein Engineering, Design and Selection

December 2000; p ublished online December 2000 .

Journal Article. Subjects: Proteins. 4761 words.

An improved antibody modelling algorithm has been developed which incorporates significant improvements to the earlier versions developed by Martin et al. (1989, 1991), Pedersen et al. (199...

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GPS 2.1: enhanced prediction of kinase-specific phosphorylation sites with an algorithm of motif length selection

Yu Xue, Zexian Liu, Jun Cao, Qian Ma, Xinjiao Gao, Qingqi Wang, Changjiang Jin, Yanhong Zhou, Longping Wen and Jian Ren.

in Protein Engineering, Design and Selection

March 2011; p ublished online November 2010 .

Journal Article. Subjects: Proteins. 3796 words.

As the most important post-translational modification of proteins, phosphorylation plays essential roles in all aspects of biological processes. Besides experimental approaches,...

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A Web-based classification system of DNA-binding protein families

M. Karmirantzou and S.J. Hamodrakas.

in Protein Engineering, Design and Selection

July 2001; p ublished online July 2001 .

Journal Article. Subjects: Proteins. 4881 words.

Rational classification of proteins encoded in sequenced genomes is critical for making the genome sequences maximally useful for functional and evolutionary studies. The family of...

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Large-scale modelling as a route to multiple surface comparisons of the CCP module family

Dinesh C. Soares, Dietlind L. Gerloff, Neil R. Syme, Andrew F.W. Coulson, John Parkinson and Paul N. Barlow.

in Protein Engineering, Design and Selection

August 2005; p ublished online June 2005 .

Journal Article. Subjects: Proteins. 6286 words.

Numerous mammalian proteins are constructed from a limited repertoire of module-types. Proteins belonging to the regulators of complement activation family—crucial for ensuring a...

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Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data

Catherine Kehl, Andrew M. Simms, Rudesh D. Toofanny and Valerie Daggett.

in Protein Engineering, Design and Selection

June 2008; p ublished online April 2008 .

Journal Article. Subjects: Proteins. 6472 words.

The Dynameomics project is our effort to characterize the native-state dynamics and folding/unfolding pathways of representatives of all known protein folds by way of molecular dynamics...

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CSS-Palm 2.0: an updated software for palmitoylation sites prediction

Jian Ren, Longping Wen, Xinjiao Gao, Changjiang Jin, Yu Xue and Xuebiao Yao.

in Protein Engineering, Design and Selection

November 2008; p ublished online August 2008 .

Journal Article. Subjects: Proteins. 3987 words.

Protein palmitoylation is an essential post-translational lipid modification of proteins, and reversibly orchestrates a variety of cellular processes. Identification of palmitoylated...

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Retro operation on the Trp-cage miniprotein sequence produces an unstructured molecule capable of folding similar to the original only upon 2,2,2-trifluoroethanol addition

Jiří Vymětal, Sreenivas Reddy Bathula, Jiří Černý, Radka Chaloupková, Lukáš Žídek, Vladimír Sklenář and Jiří Vondrášek.

in Protein Engineering, Design and Selection

December 2014; p ublished online October 2014 .

Journal Article. Subjects: Proteins. 5839 words.

Amino acid sequence and environment are the most important factors determining the structure, stability and dynamics of proteins. To evaluate their roles in the process of folding, we...

Exploring the interplay between experimental methods and the performance of predictors of binding affinity change upon mutations in protein complexes

Cunliang Geng, Anna Vangone and Alexandre M.J.J. Bonvin.

in Protein Engineering, Design and Selection

August 2016; p ublished online July 2016 .

Journal Article. Subjects: Proteins. 4650 words.

Reliable prediction of binding affinity changes (ΔΔG) upon mutations in protein complexes relies not only on the performance of computational methods but also on the availability and...