| Q30388027 | A benchmark testing ground for integrating homology modeling and protein docking |
| Q36666352 | A critical assessment of information-guided protein-protein docking predictions |
| Q42143961 | A machine learning approach for the prediction of protein surface loop flexibility |
| Q36459249 | A method for integrative structure determination of protein-protein complexes |
| Q41711426 | A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy |
| Q41788143 | A nonredundant structure dataset for benchmarking protein-RNA computational docking |
| Q30415187 | A protein-RNA docking benchmark (II): extended set from experimental and homology modeling data |
| Q28487957 | A unified conformational selection and induced fit approach to protein-peptide docking |
| Q91143383 | Accelerated Structural Prediction of Flexible Protein-Ligand Complexes: The SLICE Method |
| Q37871850 | Accounting for large amplitude protein deformation during in silico macromolecular docking. |
| Q40814679 | Accounting for observed small angle X-ray scattering profile in the protein-protein docking server ClusPro |
| Q39644733 | Accounting for pairwise distance restraints in FFT-based protein-protein docking. |
| Q34205089 | Active site coupling in PDE:PKA complexes promotes resetting of mammalian cAMP signaling |
| Q42091180 | Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges |
| Q59042601 | Advances in Human Biology: Combining Genetics and Molecular Biophysics to Pave the Way for Personalized Diagnostics and Medicine |
| Q35656554 | Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta |
| Q36307273 | Application of asymmetric statistical potentials to antibody-protein docking |
| Q39729875 | Application of information theory to feature selection in protein docking |
| Q34257699 | Arbitrary protein-protein docking targets biologically relevant interfaces. |
| Q47909076 | Assessing the reconstruction of macromolecular assemblies with toleranced models |
| Q33988409 | Benchmarking and analysis of protein docking performance in Rosetta v3.2. |
| Q35905559 | Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach |
| Q58702667 | Bioinformatics Tools and Benchmarks for Computational Docking and 3D Structure Prediction of RNA-Protein Complexes |
| Q90709301 | Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment |
| Q36090741 | Blind prediction of interfacial water positions in CAPRI |
| Q47584313 | Blind predictions of protein interfaces by docking calculations in CAPRI |
| Q36014090 | CLUB-MARTINI: Selecting Favourable Interactions amongst Available Candidates, a Coarse-Grained Simulation Approach to Scoring Docking Decoys. |
| Q33862804 | CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK. |
| Q30387722 | CSAR 2014: A Benchmark Exercise Using Unpublished Data from Pharma |
| Q27702220 | CSAR Benchmark Exercise 2013: Evaluation of Results from a Combined Computational Protein Design, Docking, and Scoring/Ranking Challenge |
| Q47364291 | Cell-Dock: high-performance protein-protein docking. |
| Q51342935 | Characterizing the morphology of protein binding patches. |
| Q28299590 | Computational modeling of protein-RNA complex structures |
| Q39780607 | Computational prediction and analysis of the DR6-NAPP interaction |
| Q38536626 | Conserved Functional Motifs and Homology Modeling to Predict Hidden Moonlighting Functional Sites |
| Q33957280 | DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking |
| Q29038132 | DockRank: Ranking docked conformations using partner-specific sequence homology-based protein interface prediction |
| Q30008752 | Docking and molecular dynamics simulations of the Fyn-SH3 domain with free and phospholipid bilayer-associated 18.5-kDa myelin basic protein (MBP)-Insights into a noncanonical and fuzzy interaction |
| Q34285002 | Docking server for the identification of heparin binding sites on proteins |
| Q38312001 | Docking, scoring, and affinity prediction in CAPRI. |
| Q30010117 | Domain-mediated protein interaction prediction: From genome to network |
| Q36949881 | Ensemble-based characterization of unbound and bound states on protein energy landscape |
| Q38976083 | Expanding the horizons of G protein-coupled receptor structure-based ligand discovery and optimization using homology models. |
| Q36470096 | Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization. |
| Q47863018 | Fast and accurate grid representations for atom-based docking with partner flexibility |
| Q47566942 | FlexPepDock lessons from CAPRI peptide-protein rounds and suggested new criteria for assessment of model quality and utility |
| Q31033753 | Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches. |
| Q51168227 | Flexible docking and refinement with a coarse-grained protein model using ATTRACT. |
| Q36746240 | Focused grid-based resampling for protein docking and mapping |
| Q30387519 | Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins |
| Q27313430 | G-actin guides p53 nuclear transport: potential contribution of monomeric actin in altered localization of mutant p53. |
| Q26858969 | GWIDD: a comprehensive resource for genome-wide structural modeling of protein-protein interactions |
| Q30400859 | GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure |
| Q42403433 | Global and local structural similarity in protein-protein complexes: implications for template-based docking |
| Q35658208 | Hierarchical Conformational Analysis of Native Lysozyme Based on Sub-Millisecond Molecular Dynamics Simulations |
| Q37601847 | How good is automated protein docking? |
| Q28728507 | How many protein-protein interactions types exist in nature? |
| Q42695812 | INTerface Builder: a fast protein-protein interface reconstruction tool |
| Q51168223 | Improved flexible refinement of protein docking in CAPRI rounds 22-27. |
| Q38666495 | Integrating atom-based and residue-based scoring functions for protein-protein docking |
| Q38192759 | Integrative computational modeling of protein interactions |
| Q104073522 | Integrative modeling of membrane-associated protein assemblies |
| Q34338720 | Integrative structural modeling with small angle X-ray scattering profiles |
| Q51012522 | InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution. |
| Q36192780 | Introducing a Clustering Step in a Consensus Approach for the Scoring of Protein-Protein Docking Models |
| Q44990288 | Intuitive, but not simple: including explicit water molecules in protein-protein docking simulations improves model quality. |
| Q38440719 | KBDOCK 2013: a spatial classification of 3D protein domain family interactions. |
| Q90189804 | Less Is More: Coarse-Grained Integrative Modeling of Large Biomolecular Assemblies with HADDOCK |
| Q92657954 | LightDock goes information-driven |
| Q30655327 | MEGADOCK: an all-to-all protein-protein interaction prediction system using tertiary structure data |
| Q55708909 | Modeling Protein Complexes Using Restraints from Crosslinking Mass Spectrometry. |
| Q43619967 | Modeling of proteins and their assemblies with the Integrative Modeling Platform |
| Q41621308 | Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology |
| Q39172517 | Modeling protein-protein and protein-peptide complexes: CAPRI 6th edition |
| Q26743663 | Molecular docking as a popular tool in drug design, an in silico travel |
| Q30398315 | Monte Carlo replica-exchange based ensemble docking of protein conformations |
| Q92955125 | More efficient screening of protein-protein complex model structures for reducing the number of candidates |
| Q37974157 | Multiscale modeling of macromolecular biosystems |
| Q66680689 | Mutagenesis of DsbAss is Crucial for the Signal Recognition Particle Mechanism in : Insights from Molecular Dynamics Simulations |
| Q39114594 | New additions to the ClusPro server motivated by CAPRI. |
| Q55120605 | Next challenges in protein-protein docking: from proteome to interactome and beyond |
| Q38067023 | On the binding affinity of macromolecular interactions: daring to ask why proteins interact |
| Q51508072 | On the use of distance constraints in protein-protein docking computations. |
| Q40604291 | Optimization of protein-protein docking for predicting Fc-protein interactions. |
| Q35045263 | PAIRpred: partner-specific prediction of interacting residues from sequence and structure |
| Q36082390 | PPCheck: A Webserver for the Quantitative Analysis of Protein-Protein Interfaces and Prediction of Residue Hotspots |
| Q35075575 | PRUNE and PROBE--two modular web services for protein-protein docking. |
| Q31043905 | Partner-aware prediction of interacting residues in protein-protein complexes from sequence data |
| Q35849095 | Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures |
| Q45949461 | Predicting protein conformational changes for unbound and homology docking: learning from intrinsic and induced flexibility. |
| Q38123046 | Prediction of RNA binding proteins comes of age from low resolution to high resolution |
| Q30387414 | Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment |
| Q58428610 | Prediction of protein binding sites and hot spots |
| Q57227082 | Predictions of protein-RNA interactions |
| Q26749162 | Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics |
| Q34163491 | Protein docking by the interface structure similarity: how much structure is needed? |
| Q34122970 | Protein docking prediction using predicted protein-protein interface |
| Q51151900 | Protein docking using case-based reasoning. |
| Q35568698 | Protein docking with predicted constraints |
| Q41842857 | Protein flexibility, not disorder, is intrinsic to molecular recognition |
| Q47382465 | Protein-ligand docking using FFT based sampling: D3R case study |
| Q39245081 | Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI. |
| Q33956399 | Protein-protein complex structure predictions by multimeric threading and template recombination |
| Q37781287 | Protein-protein docking tested in blind predictions: the CAPRI experiment |
| Q47314493 | Protein-protein interaction specificity is captured by contact preferences and interface composition |
| Q92237069 | Pushing the accuracy limit of shape complementarity for protein-protein docking |
| Q55120704 | Quantitative use of chemical shifts for the modeling of protein complexes |
| Q51050723 | Ranking multiple docking solutions based on the conservation of inter-residue contacts. |
| Q34979501 | Replica exchange improves sampling in low-resolution docking stage of RosettaDock |
| Q35075670 | Rosetta FlexPepDock web server--high resolution modeling of peptide-protein interactions |
| Q51564257 | SDOCK: a global protein-protein docking program using stepwise force-field potentials. |
| Q60211941 | Sampling Native-like Structures of RNA-Protein Complexes through Rosetta Folding and Docking |
| Q27010280 | Sampling and scoring: a marriage made in heaven |
| Q46115863 | Score_set: a CAPRI benchmark for scoring protein complexes |
| Q33756620 | Scoring docking conformations using predicted protein interfaces. |
| Q34774628 | Side-chain conformational changes upon Protein-Protein Association |
| Q34691921 | Solvated protein-DNA docking using HADDOCK. |
| Q55120528 | Solvated protein-protein docking using Kyte-Doolittle-based water preferences |
| Q41844310 | Structural templates for modeling homodimers |
| Q47567198 | Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30. |
| Q37699214 | Template-based structure modeling of protein-protein interactions |
| Q36066271 | Templates are available to model nearly all complexes of structurally characterized proteins |
| Q39024817 | The ClusPro web server for protein-protein docking |
| Q47414206 | The challenge of modeling protein assemblies: The CASP12-CAPRI experiment. |
| Q43000306 | The targets of CAPRI Rounds 13-19. |
| Q48060301 | Update of the ATTRACT force field for the prediction of protein-protein binding affinity |
| Q51152599 | Using a consensus approach based on the conservation of inter-residue contacts to rank CAPRI models. |
| Q36095634 | Variability in docking success rates due to dataset preparation |
| Q92748260 | iScore: a novel graph kernel-based function for scoring protein-protein docking models |
| Q41035490 | pyDockSAXS: protein-protein complex structure by SAXS and computational docking |