Flexible structure alignment by chaining aligned fragment pairs allowing twists

No abstract is available for this paper.

• Publication year

  2003

• Venue

  European Conference on Computational Biology

• Publication date

  2003-09-27

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1093/bioinformatics/btg1086PMID 14534198
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Analysis of interactive packing of secondary structural elements in α/β units in proteins

  2008cited by this paper
• MolMovDB: analysis and visualization of conformational change and structural flexibility

  2003cited by this paper
• Evolution of protein structures and functions.

  2002cited by this paper
• Flexible protein alignment and hinge detection

  2002influential reference
• Caught in the act: the structure of phosphorylated beta-phosphoglucomutase from Lactococcus lactis.

  2002cited by this paper
• Advanced pairwise structure alignments of proteins and analysis of conformational changes

  2002cited by this paper
• Protein flexibility predictions using graph theory

  2001cited by this paper
• Structure Comparison and Structure Patterns

  2000cited by this paper
• ProSup: a refined tool for protein structure alignment.

  2000cited by this paper
• Crystal Structures of Reaction Intermediates ofl-2-Haloacid Dehalogenase and Implications for the Reaction Mechanism*

  1998cited by this paper
• Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.

  1998influential reference
• Protein domain movements: detection of rigid domains and visualization of hinges in comparisons of atomic coordinates

  1997cited by this paper
• A mutant form of the ribosomal protein L1 reveals conformational flexibility

  1997influential reference
• Crystal structures of adenylosuccinate synthetase from Escherichia coli complexed with GDP, IMP hadacidin, NO3-, and Mg2+.

  1996cited by this paper
• Assessing the performance of fold recognition methods by means of a comprehensive benchmark.

  1996influential reference
• Optimum superimposition of protein structures: ambiguities and implications.

  1996cited by this paper
• Threading a database of protein cores

  1995influential reference
• SCOP: a structural classification of proteins database for the investigation of sequences and structures.

  1995cited by this paper
• Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins.

  1995cited by this paper
• Structural mechanisms for domain movements in proteins.

  1994cited by this paper
• Protein structure comparison by alignment of distance matrices.

  1993influential reference
• Packing of secondary structural elements in proteins. Analysis and prediction of inter-helix distances.

  1993cited by this paper
• Detection of common three‐dimensional substructures in proteins

  1991cited by this paper
• Structural and functional aspects of domain motions in proteins.

  1984cited by this paper
• Principles of Protein Structure

  1979cited by this paper
• Internal motion in globular proteins

  1978cited by this paper
• Evolution of protein structures and functions

  year unknowncited by this paper

• Conserved Roles of Sp1 in Zebrafish Development and Early Organogenesis

  2026cites this paper
• Structural analysis of a membrane‐associated delta‐6 fatty acid desaturase from Prorocentrum micans

  2025cites this paper
• HSV1 glycoprotein D utilizes an LY6-like binding domain to inhibit alpha7 nicotinic receptors

  2025cites this paper
• Engineering an indoleamine 2,3-dioxygenase immunotherapy via selective cysteine-to-serine mutations

  2025cites this paper
• Unveiling the Plasmodium inositol (pyro)phosphate pathway: Highlighting inositol polyphosphate multikinase as a novel therapeutic target for malaria

  2025cites this paper
• Generation of inositol polyphosphates through a phospholipase C-independent pathway involving carbohydrate and sphingolipid metabolism in Trypanosoma cruzi

  2025cites this paper
• Comparative structural analysis of host proteins involved in SARS-CoV-2 infection

  2025cites this paper
• The Genetic Determinants of Extreme UV Radiation and Desiccation Tolerance in a Bacterium Recovered from the Stratosphere

  2025cites this paper
• Characterization of Potential Virus Resistance Genes in Different Crops Through In-silico Approaches

  2025cites this paper
• A bivalent self-amplifying RNA vaccine against yellow fever and Zika viruses

  2025cites this paper
• Computational characterization of the xanthan gum glycosyltransferase GumK

  2025cites this paper
• Faster and More Accurate Estimation of Protein Hinges Based on Information Criteria

  2025cites this paper
• Adaptive deletion of functional duplicate genes in Drosophila

  2025cites this paper
• Comparative Study of Lefaxin Family in Two Asian Leeches: Hirudinaria manillensis and Whitmania pigra

  2025cites this paper
• Novel Method for Prioritizing Protein Binding Sites Using Pocket Analysis and MD Simulations

  2025cites this paper
• Discovery of diverse and high-quality mRNA capping enzymes through a language model–enabled platform

  2025cites this paper
• Proteins with proximal-distal asymmetries in axoneme localisation control flagellum beat frequency

  2024cites this paper
• Decoding the Granular Puzzle of Macromolecules: Efficient 3D Protein Structure Alignment in the Age of Big Data with Apache Spark

  2024cites this paper
• Protein embedding based alignment

  2024cites this paper
• TM-search: An Efficient and Effective Tool for Protein Structure Database Search

  2024cites this paper
• I’m Walking into Spiderwebs: Making Sense of Protein–Protein Interaction Data

  2024cites this paper
• Enhancing cryo-EM structure prediction with DeepTracer and AlphaFold2 integration

  2024cites this paper
• Detection of circular permutations by Protein Language Models

  2024cites this paper
• Global atlas of predicted functional domains in Legionella pneumophila Dot/Icm translocated effectors

  2024cites this paper
• Saccharibacteria deploy two distinct Type IV pili, driving episymbiosis, host competition, and twitching motility

  2024cites this paper
• Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

  2024cites this paper
• Secreted novel AID/APOBEC-like deaminase 1 (SNAD1) – a new important player in fish immunology

  2024cites this paper
• GTalign: spatial index-driven protein structure alignment, superposition, and search

  2024cites this paper
• Structural basis for the allosteric behaviour and substrate specificity of Lactococcus lactis Prolidase.

  2024cites this paper
• The glycine-rich domain of GRP7 plays a crucial role in binding long RNAs and facilitating phase separation

  2024cites this paper
• Data-Driven Modeling and Analysis of Fatty Acid Desaturase in Plants

  2023cites this paper
• FGF19 and its analog Aldafermin cooperate with MYC to induce aggressive hepatocarcinogenesis

  2023cites this paper
• Potentially Highly Effective Drugs for COVID-19: Virtual Screening and Molecular Docking Study Through PyRx-Vina Approach

  2023cites this paper
• Broad protective vaccination against systemic Escherichia coli with autotransporter antigens

  2023influential citation
• ICARUS: flexible protein structural alignment based on Protein Units

  2023cites this paper
• GradPose: a very fast and memory-efficient gradient descent-based tool for superimposing millions of protein structures from computational simulations

  2023cites this paper
• An informatic workflow for the enhanced annotation of excretory/secretory proteins of Haemonchus contortus

  2023cites this paper
• Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2

  2023cites this paper
• Bioinformatics characterization of BcsA-like orphan proteins suggest they form a novel family of pseudomonad cyclic-β-glucan synthases

  2023cites this paper
• Reductive Release from a Hybrid PKS-NRPS during the Biosynthesis of Pyrichalasin H.

  2023cites this paper
• Structure-guided mutagenesis of the capsid protein indicates that a nanovirus requires assembled viral particles for systemic infection

  2023cites this paper
• Protein Structure Refinement via DeepTracer and AlphaFold2

  2023cites this paper
• Hybrid heuristics: for the repetition-free longest common subsequence problem with index-gene

  2023cites this paper
• Reducing the assemblies of amyloid-beta multimers by sodium dodecyl sulfate surfactant at concentrations lower than critical micelle concentration: molecular dynamics simulation exploration

  2023cites this paper
• Insight into biosorption of hexavalent chromium using isolated species Aspergillus Proliferans LA: A systemic and In silico studies

  2023cites this paper
• Candida parapsilosis carbonyl reductase as a tool for preliminary screening of inhibitors for alcohol dehydrogenase induced skin sensitization

  2023cites this paper
• (S)-specific carbonyl reductase from Candida parapsilosis ATCC 7330 as a model for the initial screening of inhibitors for human carbonyl reductase

  2023cites this paper
• AlphaFold Blindness to Topological Barriers Affects Its Ability to Correctly Predict Proteins’ Topology

  2023cites this paper
• Structural Outlier Detection and Zernike–Canterakis Moments for Molecular Surface Meshes—Fast Implementation in Python

  2023cites this paper
• Spt6 directly interacts with Cdc73 and is required for Paf1 complex occupancy at active genes in Saccharomyces cerevisiae

  2023cites this paper
• The small molecule inhibitor NAV-2729 has a complex target profile including multiple ADP-ribosylation factor regulatory proteins

  2023cites this paper
• Natural variation in Avr3D1 from Zymoseptoria sp. contributes to quantitative gene-for-gene resistance and to host specificity.

  2022cites this paper
• In silico modeling human VPS13 proteins associated with donor and target membranes suggests lipid transfer mechanisms

  2022cites this paper
• A CRISPR/Cas9-engineered avatar mouse model of monocarboxylate transporter 8 deficiency displays distinct neurological alterations.

  2022cites this paper
• Molecular Recognition of FDA-Approved Small Molecule Protein Kinase Drugs in Protein Kinases

  2022cites this paper
• Improving Lipid Production of Yarrowia lipolytica by the Aldehyde Dehydrogenase-Mediated Furfural Detoxification

  2022cites this paper
• What Makes GPCRs from Different Families Bind to the Same Ligand?

  2022influential citation
• Starships are active eukaryotic transposable elements mobilized by a new family of tyrosine recombinases

  2022cites this paper
• Evidence that nuclear receptors are related to terpene synthases

  2022cites this paper
• Analysis of Integrin αIIb Subunit Dynamics Reveals Long-Range Effects of Missense Mutations on Calf Domains

  2022cites this paper
• Soluble Diphtheria Toxin Variant, CRM 197 Was Obtained in Escherichia coli at High Productivity Using SUMO Fusion and an Adjusted Expression Strategy.

  2022cites this paper
• Enhanced expression of plasma membrane intrinsic protein 2 improves cotton fiber length in Gossypium arboreum

  2022cites this paper
• Spt6 directly interacts with Cdc73 and is required for Paf1C recruitment to active genes

  2022cites this paper
• Investigation of the Importance of Protein 3D Structure for Assessing Conservation of Lysine Acetylation Sites in Protein Homologs

  2022cites this paper
• Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds

  2021cites this paper
• Metabolomics and computational analysis of the role of monoamine oxidase activity in delirium and SARS-COV-2 infection

  2021cites this paper
• Database exploration: Selection and analysis of target protein structures

  2021cites this paper
• Ancient gene duplications in RNA viruses revealed by protein tertiary structure comparisons

  2021cites this paper
• Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl

  2021cites this paper
• Identification of unknown proteins in X-ray crystallography and cryo-EM

  2021cites this paper
• findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM

  2021cites this paper
• Functional Annotation from Structural Homology.

  2021cites this paper
• Structural dynamics in the evolution of a bilobed protein scaffold

  2021cites this paper
• Enhanced Expression of Plasma Membrane Intrinsic Protein 2 Improves Cotton Fiber Length and Potential Economic Viability of Gossypium Arboreum

  2021cites this paper
• Molecular Docking Studies of ROS Agent from Quinone Family to Reductase Enzymes:Implication in Finding Anticancer Drug Candidate

  2021cites this paper
• Novel putative polyethylene terephthalate (PET) plastic degrading enzymes from the environmental metagenome

  2021cites this paper
• Proteomic analysis of archaeological ceramics from Tell Khaiber, southern Iraq

  2021cites this paper
• NMR structure and dynamics of Q4DY78, a conserved kinetoplasid-specific protein from Trypanosoma cruzi.

  2021cites this paper
• Integration of 3D Structural and Sequence Features to Predict GPCR Ligand Binding

  2021influential citation
• Evidence that nuclear receptors evolved from terpene synthases

  2021cites this paper
• Dynamic interactions of CbiN and CbiM trigger activity of a cobalt energy-coupling-factor transporter.

  2020cites this paper
• Roles of the N-terminal domain and remote substrate binding subsites in activity of the debranching barley limit dextrinase.

  2020cites this paper
• Protein Construction-Based Data Partitioning Scheme for Alignment of Protein Macromolecular Structures Through Distributed Querying in Federated Databases

  2020cites this paper
• Hierarchical Graph Representation of Pharmacophore Models

  2020cites this paper
• Human cathepsin X/Z is a biologically active homodimer.

  2020cites this paper
• Agrobacterium tumefaciens Deploys a Versatile Antibacterial Strategy To Increase Its Competitiveness

  2020cites this paper
• Deep learning model predicts water interaction sites on the surface of proteins using limited-resolution data.

  2020cites this paper
• Protein Engineering of Mung Bean (Vigna radiata (L.) Wilczek) 8Sα Globulin with Lactostatin

  2020cites this paper
• Identification of promising molecules against MurD ligase from Acinetobacter baumannii: insights from comparative protein modelling, virtual screening, molecular dynamics simulations and MM/PBSA analysis

  2020cites this paper
• Evolution of structural dynamics in bilobed proteins

  2020cites this paper
• The biological and pharmacological allosteric modulation of inositol monophosphatase

  2020cites this paper
• Benchmarking Methods of Protein Structure Alignment

  2020cites this paper
• Novel peptide ligands for antibody purification provide superior clearance of host cell protein impurities.

  2020cites this paper
• QTL detection and putative candidate gene prediction for leaf rolling under moisture stress condition in wheat

  2020cites this paper
• Potential involvement of monoamine oxidase activity in SARS-COV2 infection and delirium onset

  2020cites this paper
• Potential involvement of monoamine oxidase activity in delirium onset and SARS-COV2 infection

  2020influential citation
• Crystal structure of Q4D6Q6, a conserved kinetoplastid-specific protein from Trypanosoma cruzi.

  2020cites this paper
• A Review of Deep Learning Methods for Antibodies

  2020cites this paper
• Structure of a filamentous virus uncovers familial ties within the archaeal virosphere

  2020cites this paper
• Convolutional Neural Networks for 3D Protein Classification

  2020cites this paper