Servers for sequence–structure relationship analysis and prediction

• Published in: Nucleic acids research Vol. 31; no. 13; pp. 3359 - 3363
• Main Authors: Dosztányi, Zsuzsanna, Magyar, Csaba, Tusnády, Gábor E., Cserző, Miklós, Fiser, András, Simon, István
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.07.2003; Oxford Publishing Limited (England)
• Subjects: Algorithms; Amino Acids - chemistry; Cysteine - chemistry; Internet; Membrane Proteins - chemistry; Molecular Sequence Data; Oxidation-Reduction; Proteins - chemistry; Proteins - physiology; Sequence Analysis, Protein - methods; Software
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkg589

We describe several algorithms and public servers that were developed to analyze and predict various features of protein structures. These servers provide information about the covalent state of cysteine (CYSREDOX), as well as about residues involved in non-covalent cross links that play an important role in the structural stability of proteins (SCIDE and SCPRED). We also discuss methods and servers developed to identify helical transmembrane proteins from large databases and rough genomic data, including two of the most popular transmembrane prediction methods, DAS and HMMTOP. Several biologically interesting applications of these servers are also presented. The servers are available through http://www.enzim.hu/servers.html.