• MODELLER

  • Referenced in 33 articles [sw27731]
  • MODELLER: A Program for Protein Structure Modeling. MODELLER is used for homology or comparative modeling ... hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints ... novo modeling of loops in protein structures, optimization of various models of protein structure with ... searching of sequence databases, comparison of protein structures, etc. MODELLER is available for download...
  • GOLEM

  • Referenced in 51 articles [sw24695]
  • real-world problems such as protein structure prediction and finite element mesh design. GOLEM copes...
  • PROCHECK

  • Referenced in 21 articles [sw16885]
  • check the stereochemical quality of protein structures. The PROCHECK suite of programs provides a detailed ... check on the stereochemistry of a protein structure. Its outputs comprise a number of plots ... structure as compared with well refined structures of the same resolution and also highlight regions ... assessing the quality not only of protein structures in the process of being solved...
  • I-TASSER

  • Referenced in 17 articles [sw17207]
  • TASSER: a unified platform for automated protein structure and function prediction. The iterative threading assembly ... integrated platform for automated protein structure and function prediction based on the sequence-to-structure ... function of the protein is then inferred by structurally matching the 3D models with other ... state-of-the-art protein structure and function predictions. The server is available...
  • RAPTOR

  • Referenced in 19 articles [sw09002]
  • linear programming approach to do protein 3-dimensional (3D) structure prediction via threading. Based ... contact map graph of the protein 3D structure template, the protein threading problem is formulated ... blind and public test by the protein structure prediction community, ranks RAPTOR...
  • TM-align

  • Referenced in 14 articles [sw22248]
  • align: a protein structure alignment algorithm based on TM-score. We have developed TM-align ... algorithm to identify the best structural alignment between protein pairs that combines the TM-score ... against-all structure comparison of 10 515 representative protein chains from the Protein Data Bank ... assist in model selection in blind protein structure predictions. The TM-align program is freely...
  • PSIPRED

  • Referenced in 14 articles [sw11340]
  • PSIPRED protein structure prediction server. The PSIPRED protein structure prediction server allows users to submit ... protein sequence, perform a prediction of their choice and receive the results of the prediction ... their sequence: PSIPRED, a highly accurate secondary structure prediction method; MEMSAT 2, a new version...
  • PDB2PQR

  • Referenced in 33 articles [sw13087]
  • missing atomic coordinates to molecular structures from the Protein Data Bank and the assignment...
  • MAMMOTH

  • Referenced in 10 articles [sw26215]
  • comparison. Advances in structural genomics and protein structure prediction require the design of automatic, fast ... that allows comparison of an experimental protein structure with an arbitrary low-resolution protein tertiary ... that it can describe random structural alignments of proteins with different folds with good accuracy ... will be a good tool for protein structure comparisons in structural genomics applications. MAMMOTH...
  • DYANA

  • Referenced in 11 articles [sw08628]
  • calculation of three-dimensional protein structures from NMR data. For this application of TAD, unbiased ... sampling of conformation space in protein structure calculations with the TAD algorithm implemented ... residues, and the globular protein Antennapedia (C39S) homeodomain, which comprises unstructured polypeptide segments ... have good sampling properties for calculating protein structures that are well-constrained by experimental...
  • propy

  • Referenced in 27 articles [sw22402]
  • analysing and predicting structural, functional, expression and interaction profiles of proteins and peptides. To facilitate ... calculating the widely used structural and physicochemical features of proteins and peptides from amino acid ... descriptors, composition, transition and distribution of various structural and physicochemical properties and two types...
  • PseAAC-General

  • Referenced in 16 articles [sw22430]
  • represent protein sequences in predicting protein structural and functional attributes. We developed the program PseAAC ... able to facilitate the extensive studies on proteins and peptides. The PseAAC-General is freely...
  • VMD

  • Referenced in 83 articles [sw18651]
  • read standard Protein Data Bank (PDB) files and display the contained structure. VMD provides...
  • PSICO

  • Referenced in 10 articles [sw10910]
  • PSICO: Solving protein structures with constraint programming and optimization. In this paper we propose PSICO ... constraint-based approach to determining protein structures compatible with distance constraints obtained from Nuclear Magnetic ... case with experimental data on the dimeric protein Desulforedoxin, the method proposed here supplied similar ... reduce computation time, a major advantage because structural NMR technique generally demands multiple runs...
  • PROFEAT

  • Referenced in 14 articles [sw16924]
  • server for computing structural and physicochemical features of proteins and peptides from amino acid sequence ... Sequence-derived structural and physicochemical features have frequently been used in the development of statistical ... learning models for predicting proteins and peptides of different structural, functional and interaction profiles. PROFEAT ... computing commonly-used structural and physicochemical features of proteins and peptides from amino acid sequence...
  • iCDI-PseFpt

  • Referenced in 15 articles [sw30067]
  • determine whether a drug and a protein ion channel are interacting with each other ... knowledge of the 3D (three-dimensional) structure of protein, unfortunately their usage is quite limited ... because the 3D structures for most protein ion channels are still unknown. With the avalanche...
  • SWISS-MODEL

  • Referenced in 14 articles [sw17373]
  • comparative modeling of three-dimensional (3D) protein structures. It pioneered the field of automated modeling ... computed 120 000 user requests for 3D protein models. SWISS-MODEL provides several levels ... only an amino acid sequence of a protein is submitted to build a 3D model ... DeepView (Swiss-PdbViewer), an integrated sequence-to-structure workbench. All models are sent back...
  • SMART

  • Referenced in 16 articles [sw17187]
  • completed metazoan genomes. SMART now uses predicted proteins from complete genomes in its source sequence ... exon structure within the context of protein domain structure, and to align these displays...
  • Quat-2L

  • Referenced in 15 articles [sw22469]
  • server for predicting protein quaternary structural attributes. By hybridizing the functional-domain and sequence-correlated ... developed for predicting the quaternary structural attribute of a protein according to its sequence information...
  • QMEAN

  • Referenced in 7 articles [sw17377]
  • estimation is an essential component of protein structure prediction, since ultimately the accuracy ... applications. Usually, in the course of protein structure prediction a set of alternative models...