• ArchPRED

  • Referenced in 2 articles [sw17375]
  • loops extracted from freshly deposited new protein folds the current method outperformed...
  • PyRosetta

  • Referenced in 2 articles [sw35230]
  • implemented for algorithms demonstrating protein docking, protein folding, loop modeling and design. Availability: PyRosetta...
  • MSMBuilder

  • Referenced in 2 articles [sw23802]
  • simulations of biomolecular dynamics such as protein folding and conformational change. MSMBuilder is named...
  • PSICOV

  • Referenced in 5 articles [sw17010]
  • critical for maintaining the native fold of a protein, remains an open problem...
  • ProFASi

  • Referenced in 1 article [sw30576]
  • ProFASi: The Protein Folding and Aggregation Simulator. PROFASI (PROtein Folding and Aggregation SImulator ... program package for Monte Carlo simulations of proteins. It provides a set of tools...
  • iMOT

  • Referenced in 1 article [sw32855]
  • significant sequence similarity between proteins of similar fold and function despite poor overall sequence identity ... interacting motifs among distantly related proteins sharing similar folds and possessing common ancestral lineage. Spatial ... should also be of value in protein folding, modelling and engineering experiments. The iMOT server...
  • QUB

  • Referenced in 3 articles [sw22010]
  • been used to model molecular motors, protein (un)folding, fluorescent emitters, DNA transport, and more...
  • Euk-PLoc

  • Referenced in 24 articles [sw22420]
  • avoid the homology bias, none of the proteins included has > or =25% sequence identity ... success rates thus obtained via the 5-fold and jackknife cross-validation tests were ... predicted by Euk-PLoc for all eukaryotic protein entries (excluding fragments) in Swiss-Prot database...
  • STING contacts

  • Referenced in 1 article [sw35653]
  • interactions, representing the forces that govern protein folding, stability and binding, is the key feature...
  • ACORD

  • Referenced in 1 article [sw03097]
  • problems, ranging from quadratic assignment to protein folding or routing vehicles...
  • HMMER

  • Referenced in 18 articles [sw10514]
  • searching. HMMER is a software suite for protein sequence similarity searches using probabilistic methods. Previously ... software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions ... been designed and implemented such that most protein database searches return within a few seconds...
  • HIT

  • Referenced in 1 article [sw35512]
  • interactions can be critical to establishing protein conformation (folding) and dynamics, as well as determining...
  • PreSSAPro

  • Referenced in 2 articles [sw00730]
  • perspective of identifying proteins able to fold in different conformations. The service is available...
  • PIBASE

  • Referenced in 2 articles [sw29350]
  • from the Structural Classification of Proteins and CATH fold classification systems. Results: PIBASE currently contains...
  • TargetSpy

  • Referenced in 2 articles [sw29586]
  • human dataset revealing fold-change in protein production for five selected microRNAs our method shows...
  • HHrep

  • Referenced in 3 articles [sw22482]
  • detect highly divergent repeat units in protein sequences whose repeats could as yet only ... structures. Examples include sequences with beta-propellor fold, ferredoxin-like ... fold, double psi barrels or (betaalpha)8 (TIM) barrels. We illustrate this with proteins from...
  • PIRSF

  • Referenced in 1 article [sw22978]
  • comparative studies of protein function and evolution. Domain or fold-based searches allow identification ... evolutionarily related protein families sharing domains or structural folds. Functional convergence and functional divergence...
  • MetaDisorder

  • Referenced in 1 article [sw16901]
  • known protein structures, reported by the protein fold-recognition methods, to infer the potentially structured...
  • PSIPRED

  • Referenced in 14 articles [sw11340]
  • prediction server allows users to submit a protein sequence, perform a prediction of their choice ... method; or GenTHREADER, a sequence profile based fold recognition method. Availability: Freely available...
  • ESLpred

  • Referenced in 20 articles [sw22403]
  • accuracies of nuclear, cytoplasmic, mitochondrial and extracellular proteins reached 95.3, 85.2, 68.2 and 88.9%, respectively ... modules was evaluated using a 5-fold cross-validation technique. Assigning a reliability index (reliability...