| scholarly article | Q13442814 |
| review article | Q7318358 |
| P50 | author | Burkhard Rost | Q4998995 |
| Lucy R. Forrest | Q57016893 | ||
| Marco Punta | Q67224348 | ||
| Jinfeng Liu | Q30348390 | ||
| P2093 | author name string | Andrew Kernytsky | |
| Henry Bigelow | |||
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| Assessment of CASP6 predictions for new and nearly new fold targets | Q28274204 | ||
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| PHD: predicting one-dimensional protein structure by profile-based neural networks | Q29614390 | ||
| A combined transmembrane topology and signal peptide prediction method | Q29615817 | ||
| A hierarchical approach to all-atom protein loop prediction | Q29615859 | ||
| The Protein Data Bank | Q29616068 | ||
| OPM: orientations of proteins in membranes database | Q29616317 | ||
| Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method | Q29616523 | ||
| SOSUI: classification and secondary structure prediction system for membrane proteins | Q29616676 | ||
| Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule | Q29616679 | ||
| A graph-theory algorithm for rapid protein side-chain prediction | Q29619249 | ||
| Interstrand pairing patterns in beta-barrel membrane proteins: the positive-outside rule, aromatic rescue, and strand registration prediction | Q30160069 | ||
| Consensus based validation of membrane porins. | Q30160295 | ||
| PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins | Q30163988 | ||
| BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria | Q30163990 | ||
| Predicting transmembrane beta-barrels in proteomes | Q30164081 | ||
| A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins | Q30165257 | ||
| kPROT: a knowledge-based scale for the propensity of residue orientation in transmembrane segments. Application to membrane protein structure prediction. | Q30324076 | ||
| Non-alpha-helical elements modulate polytopic membrane protein architecture. | Q30327963 | ||
| EVA: Evaluation of protein structure prediction servers. | Q30333046 | ||
| BPROMPT: A consensus server for membrane protein prediction | Q30333058 | ||
| Structural details (kinks and non-alpha conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors | Q30333243 | ||
| A family of evolution-entropy hybrid methods for ranking protein residues by importance. | Q30340973 | ||
| Alignment of protein sequences by their profiles | Q30341029 | ||
| Shorter side chains optimize helix-helix packing. | Q30341206 | ||
| The progress of membrane protein structure determination | Q30342003 | ||
| TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates. | Q30344223 | ||
| Identification of novel membrane proteins by searching for patterns in hydropathy profiles | Q43977215 | ||
| Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model | Q44321996 | ||
| Complex interactions at the helix-helix interface stabilize the glycophorin A transmembrane dimer | Q45112660 | ||
| A simple method for modeling transmembrane helix oligomers | Q46139248 | ||
| Identification of candidate Drosophila olfactory receptors from genomic DNA sequence | Q47069988 | ||
| STAM: simple transmembrane alignment method | Q47232217 | ||
| An evolutionarily conserved network of amino acids mediates gating in voltage-dependent potassium channels | Q47333767 | ||
| Snorkeling preferences foster an amino acid composition bias in transmembrane helices | Q47624028 | ||
| Enhanced recognition of protein transmembrane domains with prediction-based structural profiles. | Q48467132 | ||
| An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes. | Q48499694 | ||
| SVMtm: support vector machines to predict transmembrane segments. | Q51024145 | ||
| Multiple interactions between transmembrane helices generate the oligomeric alpha1b-adrenoceptor. | Q51824763 | ||
| Sequence and hydropathy profile analysis of two classes of secondary transporters. | Q51966600 | ||
| Transmembrane helix prediction: a comparative evaluation and analysis. | Q51972287 | ||
| TM or not TM: transmembrane protein prediction with low false positive rate using DAS-TMfilter. | Q52005819 | ||
| Key issues in the computational simulation of GPCR function: representation of loop domains. | Q52013586 | ||
| Reliability measures for membrane protein topology prediction algorithms. | Q52020755 | ||
| Basic charge clusters and predictions of membrane protein topology. | Q52037726 | ||
| A novel tool for the prediction of transmembrane protein topology based on a statistical analysis of the SwissProt database: the OrienTM algorithm. | Q52058097 | ||
| Statistical analysis of amino acid patterns in transmembrane helices: the GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions. | Q52081092 | ||
| A potential smoothing algorithm accurately predicts transmembrane helix packing. | Q52227464 | ||
| Estimation of structural similarity of membrane proteins by hydropathy profile alignment. | Q52243154 | ||
| Prediction of membrane protein topology utilizing multiple sequence alignments. | Q52260817 | ||
| In silico two-hybrid system for the selection of physically interacting protein pairs. | Q54547905 | ||
| A Cα Model for the Transmembrane α Helices of Gap Junction Intercellular Channels | Q57207119 | ||
| A Novel Scoring Function for Predicting the Conformations of Tightly Packed Pairs of Transmembrane α-Helices | Q57207133 | ||
| Consensus predictions of membrane protein topology | Q57381568 | ||
| Positively charged residues influence the degree of SecA dependence in protein translocation across the E. coli inner membrane | Q57381598 | ||
| Automatic methods for predicting functionally important residues | Q73009415 | ||
| Helix packing in membrane proteins | Q73878142 | ||
| Side chains in transmembrane helices are shorter at helix-helix interfaces | Q73912098 | ||
| A turn propensity scale for transmembrane helices | Q77753683 | ||
| Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling | Q79210002 | ||
| On the role of structural information in remote homology detection and sequence alignment: new methods using hybrid sequence profiles | Q79329407 | ||
| LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction. | Q30349848 | ||
| A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. | Q30350835 | ||
| Protein structure prediction: inroads to biology. | Q30352265 | ||
| Transmembrane protein structures without X-rays. | Q30352513 | ||
| A model recognition approach to the prediction of all-helical membrane protein structure and topology | Q30420917 | ||
| The GxxxG motif: a framework for transmembrane helix-helix association | Q30839523 | ||
| Folding in lipid membranes (FILM): a novel method for the prediction of small membrane protein 3D structures | Q30885873 | ||
| Transmembrane proteins in the Protein Data Bank: identification and classification. | Q30936827 | ||
| Extending the accuracy limits of prediction for side-chain conformations | Q30998288 | ||
| High-throughput modeling of human G-protein coupled receptors: amino acid sequence alignment, three-dimensional model building, and receptor library screening | Q31063961 | ||
| PRED-GPCR: GPCR recognition and family classification server | Q31081622 | ||
| Discrimination of native loop conformations in membrane proteins: decoy library design and evaluation of effective energy scoring functions. | Q31153497 | ||
| The compositional adjustment of amino acid substitution matrices | Q33195777 | ||
| Evaluation of methods for the prediction of membrane spanning regions | Q33953551 | ||
| An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins | Q33967104 | ||
| Transmembrane glycine zippers: physiological and pathological roles in membrane proteins | Q34063410 | ||
| Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction | Q34064011 | ||
| Non-symmetric score matrices and the detection of homologous transmembrane proteins | Q34085064 | ||
| Topogenic signals in integral membrane proteins | Q34167358 | ||
| PRINTS and its automatic supplement, prePRINTS. | Q34169535 | ||
| Functional analysis of an archaebacterial voltage-dependent K+ channel | Q34182941 | ||
| Classification of 29 families of secondary transport proteins into a single structural class using hydropathy profile analysis | Q34186640 | ||
| Helical packing patterns in membrane and soluble proteins. | Q34188161 | ||
| Biogenesis of inner membrane proteins in Escherichia coli | Q34222736 | ||
| Sequence specificity in the dimerization of transmembrane alpha-helices | Q34279030 | ||
| Protein database searches using compositionally adjusted substitution matrices | Q34293765 | ||
| Transmembrane helices predicted at 95% accuracy | Q34314226 | ||
| Organization of the G protein-coupled receptors rhodopsin and opsin in native membranes | Q34333541 | ||
| Modeling flexible loops in the dark-adapted and activated states of rhodopsin, a prototypical G-protein-coupled receptor | Q34352345 | ||
| Global analysis of predicted proteomes: functional adaptation of physical properties | Q34375646 | ||
| The GxxxG-containing transmembrane domain of the CCK4 oncogene does not encode preferential self-interactions | Q34389713 | ||
| P433 | issue | 4 | |
| P407 | language of work or name | English | Q1860 |
| P921 | main subject | membrane protein | Q423042 |
| P304 | page(s) | 460-74 | |
| P577 | publication date | 2007-04-01 | |
| P1433 | published in | Methods | Q6823859 |
| P1476 | title | Membrane protein prediction methods | |
| P478 | volume | 41 |
| Q38392886 | A Machine Learning Approach to Explain Drug Selectivity to Soluble and Membrane Protein Targets |
| Q59026429 | A Topology Structure Based Outer Membrane Proteins Segment Alignment Method |
| Q30428754 | A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions |
| Q36215910 | A dominant negative heterozygous G87R mutation in the zinc transporter, ZnT-2 (SLC30A2), results in transient neonatal zinc deficiency |
| Q33842208 | A folding pathway-dependent score to recognize membrane proteins |
| Q33909568 | A new in-silico method for determination of helical transmembrane domains based on the PepLook scan: application to IL-2Rβ and IL-2Rγc receptor chains. |
| Q40339702 | A novel N-terminal region of the membrane β-hexosyltransferase: its role in secretion of soluble protein by Pichia pastoris. |
| Q37578268 | Advances in the Development and Application of Computational Methodologies for Structural Modeling of G-Protein Coupled Receptors. |
| Q28474217 | Biochemical properties of gastrokine-1 purified from chicken gizzard smooth muscle |
| Q27002674 | Bioinformatics approaches for functional annotation of membrane proteins |
| Q33648848 | CLPTM1L promotes growth and enhances aneuploidy in pancreatic cancer cells |
| Q48886998 | Combining modelling and mutagenesis studies of synaptic vesicle protein 2A to identify a series of residues involved in racetam binding. |
| Q64074411 | Comparative Genomics of HRh1 and sp. SCN-R1, Halophilic Chemolithoautotrophic Sulfur-Oxidizing Capable of Using Thiocyanate as Energy Source |
| Q33836276 | Comparison of human solute carriers |
| Q30380431 | Computational analysis of membrane proteins: the largest class of drug targets. |
| Q37248350 | Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome |
| Q30419401 | Coordinating the impact of structural genomics on the human α-helical transmembrane proteome |
| Q24323157 | Defining the membrane proteome of NK cells |
| Q30401700 | Discrimination of Native-like States of Membrane Proteins with Implicit Membrane-based Scoring Functions. |
| Q30157241 | Elucidating in vivo structural dynamics in integral membrane protein by hydroxyl radical footprinting |
| Q41642290 | Evaluation of transmembrane helix predictions in 2014. |
| Q55564362 | GPCR Conformations: Implications for Rational Drug Design. |
| Q30157261 | HHomp--prediction and classification of outer membrane proteins |
| Q30155420 | Identification and localization of Myxococcus xanthus porins and lipoproteins |
| Q33368452 | IgTM: an algorithm to predict transmembrane domains and topology in proteins |
| Q34979349 | In silico mutagenesis: a case study of the melanocortin 4 receptor |
| Q41728362 | Insights into the binding modes of CC chemokine receptor 4 (CCR4) inhibitors: a combined approach involving homology modelling, docking, and molecular dynamics simulation studies |
| Q37304115 | Knowledge-based computational intelligence development for predicting protein secondary structures from sequences |
| Q33711713 | MEDELLER: homology-based coordinate generation for membrane proteins |
| Q28750585 | MPlot--a server to analyze and visualize tertiary structure contacts and geometrical features of helical membrane proteins |
| Q42735441 | Mapping the protein-protein interface between a toxin and its cognate antitoxin from the bacterial pathogen Streptococcus pyogenes |
| Q30424545 | Membrane protein native state discrimination by implicit membrane models |
| Q35515687 | Membrane topological structure of neutral system N/A amino acid transporter 4 (SNAT4) protein |
| Q54295409 | Membrane transport piece by piece: production of transmembrane peptides for structural and functional studies. |
| Q57207084 | Modeling and Validation of Transmembrane Protein Structures |
| Q33517965 | Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences |
| Q33751096 | Molecular modeling and ligand docking for solute carrier (SLC) transporters |
| Q39146244 | Predicting Alpha Helical Transmembrane Proteins Using HMMs. |
| Q45952551 | Predicting Subcellular Localization of Proteins by Bioinformatic Algorithms. |
| Q53599241 | Prediction of outer membrane proteins by combining the position- and composition-based features of sequence profiles. |
| Q45946854 | Protein Sorting Prediction. |
| Q43103617 | RHYTHM--a server to predict the orientation of transmembrane helices in channels and membrane-coils |
| Q38807834 | Reverse Vaccinology: The Pathway from Genomes and Epitope Predictions to Tailored Recombinant Vaccines. |
| Q41465545 | Simultaneous prediction of protein secondary structure and transmembrane spans |
| Q37764644 | Single-spanning transmembrane domains in cell growth and cell-cell interactions: More than meets the eye? |
| Q34276839 | Structural genomics plucks high-hanging membrane proteins |
| Q30381964 | Structural genomics target selection for the New York consortium on membrane protein structure. |
| Q30396232 | Systematic evaluation of CS-Rosetta for membrane protein structure prediction with sparse NOE restraints |
| Q57091959 | Tandem application of cationic colloidal silica and Triton X-114 for plasma membrane protein isolation and purification: Towards developing an MDCK protein database |
| Q51777326 | The basic concepts of molecular modeling. |
| Q57809312 | The state of the art of membrane protein structure prediction: from sequence to 3D structure |
| Q30352431 | Transmembrane protein alignment and fold recognition based on predicted topology |
| Q33745806 | Trichomonas vaginalis vast BspA-like gene family: evidence for functional diversity from structural organisation and transcriptomics |
| Q57091965 | Triton X-114 phase separation in the isolation and purification of mouse liver microsomal membrane proteins |
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