• E-CELL

  • Referenced in 23 articles [sw07917]
  • models for simulating intracellular molecular processes to predict the dynamic behavior of living cells. Previous ... user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene ... through a computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical...
  • BetaSCP

  • Referenced in 3 articles [sw08772]
  • Protein structure optimization by side-chain positioning via beta-complex. A molecular structure determines ... structure is important for biotechnology. The computational prediction of molecular structure is a frequent requirement ... homology modeling, a docking simulation, a protein design, etc. where the optimization of molecular structure ... core problems in the optimization of protein structure is the optimization of side-chains called...
  • TopologyNet

  • Referenced in 8 articles [sw41013]
  • success in image, video and audio processing, computer vision, and speech recognition, their applications ... hindered by the entangled geometric complexity and biological complexity. We introduce topology, i.e., element specific ... untangle geometric complexity and biological complexity. ESPH represents 3D complex geometry by one-dimensional ... topological neural network (TopologyNet) for the predictions of protein-ligand binding affinities and protein stability...
  • PREvaIL

  • Referenced in 10 articles [sw25073]
  • critical to our understanding the relationship between protein sequence, structure, function, and enhancing our ability ... catalytic residues are resource- and labor-intensive, computational approaches have considerable value and are highly ... describe a new computational method called PREvaIL for predicting enzyme catalytic residues. This method ... both understanding the complex sequence-structure-function relationships of proteins and facilitating the characterization...
  • MIGenAS

  • Referenced in 2 articles [sw36791]
  • databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein–structure prediction. Individual ... pipelines allowing the user to conveniently process complex workflows without the necessity to take care...
  • Graemlin

  • Referenced in 5 articles [sw29736]
  • networks. Recently, however, new computational techniques have produced hundreds of predicted interaction networks with interconnection ... conserved network topologies other than protein complexes and metabolic pathways. To assess Græmlin’s performance...
  • IDDI

  • Referenced in 1 article [sw29369]
  • interacting proteins. The 3D structures of complex proteins are reliable source of domain-domain interaction ... very limited. Several resources for the computationally predicted DDI have been generated but they...
  • CABIN

  • Referenced in 1 article [sw09283]
  • However, not all prediction tools and databases predict interactions with one hundred percent accuracy. Generation ... first step towards deciphering unknown protein functions, determining protein complexes and inventing drugs. The CABIN ... sources, thereby increasing the confidence of computational predictions as well as validating experimental observations. CABIN...
  • PIPE

  • Referenced in 6 articles [sw26869]
  • Protein-Protein Interaction Prediction Engine termed PIPE. This tool is capable of predicting protein-protein ... proteins from their primary structure and without the need for any additional information or predictions ... proteins. PIPE showed a sensitivity of 61% for detecting any yeast protein interaction with ... yeast proteins. This lead us to the identification of a novel yeast complex that here...
  • GalaxySite

  • Referenced in 2 articles [sw32097]
  • coordinates of the protein-ligand complexes, whereas other methods predict only identities of binding-site ... residues or copy binding geometry from similar proteins. The additional information on the specific binding ... useful for applications in functional studies and computer-aided drug discovery...
  • MARCH-INSIDE

  • Referenced in 4 articles [sw27730]
  • SIlico DEsign) is a simple but efficient computational approach to the study of Quantitative Structure ... classic sto-TIs to predict antiparasite compounds for the treatment of Fascioliasis. Next, we revised ... chiral sto-TIs (sto-CTIs) to predict new antibacterial, antiviral and anti-coccidial compounds. After ... which unifying QSAR models predicting antifungal, antibacterial, or anti-parasite drugs with multiple targets (microbial...
  • Macrodox

  • Referenced in 2 articles [sw08087]
  • user to compute and display physical properties of individual proteins and nucleic acids starting from ... coordinate information downloaded from the Protein Data Bank. Such properties would include surrounding electrostatic fields ... complexes using a Brownian dynamics algorithm and make predictions of the most energetically stable complexes ... interactions. Additionally the program is able to compute the bimolecular diffusive rate constant of attainment...
  • rpiCOOL

  • Referenced in 0 articles [sw34163]
  • random forest. Understanding the principle of RNA–protein interactions (RPIs) is of critical importance ... useful to guide studies about many complex diseases. The limitations and difficulties associated with experimental ... call an urgent need to computational methods for RPI prediction. In this paper, we proposed ... machine learning method to detect RNA–protein interactions based on sequence information. We used motif...
  • Gene3D

  • Referenced in 2 articles [sw22981]
  • chain families so as to aid functional prediction. The structural annotation is generated using ... CATH is a repository for manually deduced protein domains. Amongst the changes from the last ... from COGs, KEGG and GO, and proteinprotein interaction data from MINT and BIND ... users to carry out complex investigations at their own computers...
  • Gaggle

  • Referenced in 4 articles [sw20341]
  • microarrays, of metabolic networks and of predicted protein structure. A crucial challenge is to combine ... that does justice to the variety and complexity of systems biology data sets. A solution ... which we identify a putative ricin-like protein -a discovery made possible by simultaneous data ... experimental data (mRNA and protein abundance, protein-protein and protein-DNA interactions), functional associations (operon...
  • MoRFpred

  • Referenced in 0 articles [sw25074]
  • which motivates development of computational methods that predict MoRFs from protein chains. Results: We introduce ... MoRF types (α, β, coil and complex). We develop a comprehensive dataset of annotated MoRFs...
  • NatalieQ

  • Referenced in 1 article [sw34156]
  • taken into account to adequately model the complex behavior of biological systems. These interactions ... transduction and protein-protein interaction networks. We recently developed natalie, which computes high-quality network ... based alignment of a specified query protein-protein interaction network to a selected target network ... sequence and the network level, we compute alignments that allow for the transfer of functional...
  • NRGTEN

  • Referenced in 1 article [sw36446]
  • mode analysis of proteins, nucleic acids, small molecules and their complexes. Coarse-grained normal mode ... analysis (NMA) is a fast computational technique to study the dynamics of biomolecules. Here ... atomic interactions. This makes possible some unique predictions of the effect of mutations, such ... from a starting structure to aid in protein-protein, protein-ligand or other docking studies...
  • ModeRNA

  • Referenced in 1 article [sw17142]
  • there are numerous methods for computational prediction of protein three-dimensional (3D) structure from sequence ... successful modeling, and for large and complex RNA molecules the development of a good alignment...
  • nocoRNAc

  • Referenced in 2 articles [sw17423]
  • time-consuming, there is a need for computational methods that allow the detection of functional ... wide prediction of functional RNAs have been developed but most of them predict a genomic ... RNAc, a program for the genome-wide prediction of ncRNA transcripts in bacteria. NOCO RNAc ... transcripts most of them located antisense to protein-coding regions. Using a custom design microarray...