• ProTherm

  • Referenced in 9 articles [sw16247]
  • functional and literature information. The sequence and structural information of proteins is connected with thermodynamic...
  • FoldRate

  • Referenced in 15 articles [sw35301]
  • knowledge of their 3D (three dimensional) structures is becoming increasingly wide. It is highly desired ... proteins based on their amino acid sequence information alone. To address this problem, an ensemble ... directly obtained or easily derived from the sequences of proteins. It was demonstrated ... that, however, need both the sequence and 3D structure information for predicting the folding rate...
  • Unb-DPC

  • Referenced in 7 articles [sw25079]
  • method is fast and preserves protein sequence structure information. The experimental results yield SVM based...
  • iMethyl-PseAAC

  • Referenced in 21 articles [sw22443]
  • incorporating its physicochemical, sequence evolution, biochemical, and structural disorder information into the general form...
  • FUGUE

  • Referenced in 9 articles [sw16894]
  • global-local algorithm to align a sequence-structure pair when they greatly differ in length ... structure is determined according to its solvent accessibility, its position relative to the secondary structure ... SSEs. (3) Combined information from both multiple sequences and multiple structures. FUGUE is designed ... align multiple sequences against multiple structures to enrich the conservation/variation information. We demonstrate that...
  • PROMALS3D

  • Referenced in 3 articles [sw16918]
  • with Evolutionary and Three-Dimensional Structural Information. Multiple sequence alignment (MSA) is an essential tool ... computational task. The constantly increasing protein sequences and structures in public databases could be used ... evolutionary and structural information from database searches. PROMALS3D automatically identifies homologs from sequence and structure ... consensus alignment enriched with sequence and structural information about input proteins and their homologs. PROMALS3D...
  • Mfold

  • Referenced in 42 articles [sw12672]
  • form of structure plots with or without reliability information, single strand frequency plots and ‘energy ... available for the folding of single sequences. A variety of ‘bulk’ servers give less information...
  • T-coffee

  • Referenced in 41 articles [sw13195]
  • sequences align with each other. This alignment information can be derived from heterogeneous sources such ... mixture of alignment programs and/or structure superposition. Here, we illustrate the power of the approach ... regardless of the phylogenetic spread of the sequences in the tests...
  • Expresso

  • Referenced in 2 articles [sw12009]
  • Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Expresso ... sequence alignment server that aligns sequences using structural information. The user only needs to provide ... alignment of the original sequences based on the structural information of the templates. An advanced ... used to model each sequence. Providing the suitable structural information is available, Expresso delivers sequence...
  • PLMLA

  • Referenced in 4 articles [sw36907]
  • called PLMLA that incorporates protein sequence information, secondary structure and amino acid properties to predict ... acetylation of lysine residues in whole protein sequences. We apply an encoding scheme based ... weight amino acid composition to extract sequence information and physicochemical properties around lysine sites ... close to methylated lysine in three-dimensional structure and have a significant influence on methyllysine...
  • PREvaIL

  • Referenced in 10 articles [sw25073]
  • residues and helping to bridge the sequence-structure-function gap. In this study, we describe ... comprehensive set of informative features extracted from multiple levels, including sequence, structure, and residue-contact...
  • RSARF

  • Referenced in 5 articles [sw22442]
  • solvent accessibility gives useful insights into protein structure prediction and function prediction. In this work ... residue accessible surface area from protein sequence information. The training and testing was performed using ... residue solvent accessibility from protein sequence without using structural information. The RSARF program, datasets...
  • Quat-2L

  • Referenced in 15 articles [sw22469]
  • quaternary structural attribute of a protein according to its sequence information alone. The 1st layer...
  • 3DCoffee

  • Referenced in 7 articles [sw12008]
  • multiple sequence alignment. It has long been suspected that structural information can help to improve ... alignments, yet the effect of combining sequences and structures has not been evaluated systematically...
  • MSACompro

  • Referenced in 1 article [sw38910]
  • MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts ... Coffee) that use the tertiary structure information of some sequences since the structural information ... that incorporating predicted protein structural information improves the multiple sequence alignment accuracy over the leading ... effectively incorporate predicted protein structural information into multiple sequence alignment. The software is available...
  • GenBank

  • Referenced in 8 articles [sw28961]
  • protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information...
  • Profunc

  • Referenced in 3 articles [sw17204]
  • provides a convenient compendium of sequence and structural information that often hold vital functional clues...
  • JPred

  • Referenced in 7 articles [sw35977]
  • secondary structure prediction algorithms that exploit evolutionary information from multiple sequences. A consensus prediction ... algorithms and allows conservation patterns important to structure and function to be identified. AVAILABILITY...
  • MICAlign

  • Referenced in 2 articles [sw12010]
  • multiple sources of information in conditional random fields. Summary: Sequence-to-structure alignment in template ... multiple sources of information from local structural contexts of template, sequence profiles, predicted secondary structures...
  • PROMALS

  • Referenced in 5 articles [sw22476]
  • homologs from PSI-BLAST searches and secondary structure predictions from PSIPRED. PROMALS shows higher alignment ... colored alignment augmented with information about sequence grouping, predicted secondary structures and positional conservation...