ReviewCurrent opinion in structural biology2009
Computational design of affinity and specificity at protein-protein interfaces.
Review in Current opinion in structural biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
70 citing papers in PubMed.
- Dose-Dependent Influence of RBD-Derived Amyloidogenic Peptides on SARS-CoV-2 Infectivity: A Cautionary Tale for Antiviral Design.International journal of molecular sciences · 2026Article
- Assembly and Functionality of 2D Protein Arrays.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Review
- The genetic landscape of a metabolic interaction.Nature communications · 2024Article
- AbFlex: designing antibody complementarity determining regions with flexible CDR definition.Bioinformatics (Oxford, England) · 2024Article
- Redesigning an antibody H3 loop by virtual screening of a small library of human germline-derived sequences.Scientific reports · 2021Article
- Proteus: An algorithm for proposing stabilizing mutation pairs based on interactions observed in known protein 3D structures.BMC bioinformatics · 2020Article
- Exploration of the Substrate Preference of Lysine Methyltransferase SMYD3 by Molecular Dynamics Simulations.ACS omega · 2019Article
- EvoDesign: Designing Protein-Protein Binding Interactions Using Evolutionary Interface Profiles in Conjunction with an Optimized Physical Energy Function.Journal of molecular biology · 2019Article
- Improving T Cell Receptor On-Target Specificity via Structure-Guided Design.Molecular therapy : the journal of the American Society of Gene Therapy · 2019Article
- In Silico Engineering of Synthetic Binding Proteins from Random Amino Acid Sequences.iScience · 2019Article
- The intersection of affinity and specificity in the development and optimization of T cell receptor based therapeutics.Seminars in cell & developmental biology · 2018Review
- Peptide design by optimization on a data-parameterized protein interaction landscape.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Recent advances in automated protein design and its future challenges.Expert opinion on drug discovery · 2018Review
- DisruPPI: structure-based computational redesign algorithm for protein binding disruption.Bioinformatics (Oxford, England) · 2018Article
- RosettaAntibodyDesign (RAbD): A general framework for computational antibody design.PLoS computational biology · 2018Article
- Cyclic oligomer design with de novo αβ-proteins.Protein science : a publication of the Protein Society · 2017Article
- Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes.Journal of immunology (Baltimore, Md. : 1950) · 2017Review
- Discovery of peptide ligands through docking and virtual screening at nicotinic acetylcholine receptor homology models.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions.Bioinformatics (Oxford, England) · 2017Article
- LUTE (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
10 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
The computer-based design of protein-protein interactions is a rigorous test of our understanding of molecular recognition and an attractive approach for creating novel tools for cell and molecular research. Considerable attention has been placed on redesigning the affinity and specificity of naturally occurring interactions. Several studies have shown that reducing the desolvation costs for binding while preserving shape complimentarity and hydrogen bonding is an effective strategy for improving binding affinities. In favorable cases specificity has been designed by focusing only on interactions with the target protein, while in cases with closely related off-target proteins it has been necessary to explicitly disfavor unwanted binding partners. The rational design of protein-protein interactions from scratch is still an unsolved problem, but recent developments in flexible backbone design and energy functions hold promise for the future.
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.