Thom Vreven

Molecular Biology · 2000–2019

A researcher in the Science corpus: 13 papers; trusts 10 researchers and is trusted by 20 researchers here, as inferred from the citation graph.

Subfields

• Molecular Biology — 135 citations into it; #3,271 of 17,773 by trust here, #3,737 by citations
• Computational Theory and Mathematics — 42 citations into it; #9,494 of 12,182 by trust here, #2,419 by citations
• Computational Biology & Bioinformatics — 39 citations into it
• Radiology, Nuclear Medicine and Imaging — 19 citations into it
• Spectroscopy — 12 citations into it; #1,319 of 1,674 by trust here, #1,380 by citations
• Natural Language Processing — 5 citations into it

Whom Thom Vreven trusts overall

Their strongest outbound trust, strongest first, inferred from their citations.

1. Rong Chen
2. Zhiping Weng
3. Joël Janin
4. András Szilágyi
5. Brian G. Pierce
6. Tammy M. K. Cheng
7. Alexandre M. J. J. Bonvin
8. S. Parasuraman
9. Mieczyslaw Torchala
10. Emmanuel Paradis

Who trusts Thom Vreven overall

1. Lung Wa Chung
2. Brian G. Pierce
3. Hans Senn
4. Hajime Hirao
5. Kathryn A. Porter
6. Walter Thiel
7. Israel T. Desta
8. Ivan V. Anishchenko
9. Xin Li
10. Stephan Eismann

Papers from Thom Vreven's perspective

Ordered by how strongly the researchers Thom Vreven trusts endorse each paper. Same corpus, a different order for every researcher.

1. A protein–protein docking benchmark (Proteins: Structure, Function, and Bioinformatics)
2. TM-align: a protein structure alignment algorithm based on the TM-score
3. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing
4. Assessment of blind predictions of protein–protein interactions: Current status of docking methods
5. Prediction of protein-protein interactions by docking methods. (Current Opinion in Structural Biology)
6. Docking and scoring protein complexes: CAPRI 3rd Edition
7. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.
8. Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS) (Nature Methods)
9. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin
10. Small-molecule inhibitors of protein–protein interactions: progressing towards the dream

Their papers

• Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment (2016) — 130 citations
• Modeling T cell receptor recognition of CD1-lipid and MR1-metabolite complexes (2014) — 10 citations
• ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers (2014) — 1,649 citations
• Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment (2019) — 104 citations
• Protein–protein docking benchmark version 4.0 (2010) — 503 citations
• Updates to the integrated protein-protein interaction benchmarks: Docking benchmark version 5 and affinity benchmark version 2 (2015) — 424 citations
• Performance of ZDOCK and ZRANK in CAPRI Rounds 13 - 19 (2010) — 84 citations
• Geometry optimization with QM/MM methods II: Explicit quadratic coupling (2006) — 139 citations
• On the application of the IMOMO (integrated molecular orbital + molecular orbital) method (2000) — 417 citations
• Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOM. (2006) — 843 citations
• Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions (2013) — 102 citations
• Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints (2003) — 528 citations
• Ultrafast Radiationless Deactivation of Organic Dyes: Evidence for a Two-State Two-Mode Pathway in Polymethine Cyanines (2000) — 146 citations