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Mechanism and Catalytic Site Atlas - A database of enzyme mechanisms and active sites

Other IDs

ResearcherID: H-2474-2013
Scopus Author ID: 55941497000
Ciência ID: 471D-534E-682F
ResearcherID: JDV-5178-2023
AuthenticusID: R-000-W64

Countries

United Kingdom, Portugal

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Funding (7)

"Catalytic Predictor": An Automated Computational Tool to Characterise Enzyme Reaction Mechanisms

2023-07-01 to 2029-06-30 | Grant
Fundação para a Ciência e a Tecnologia (Lisboa, PT)
GRANT_NUMBER:

2022.03058.CEECIND
Source: check_circle
CIÊNCIAVITAE

Unidade de Ciências Biomoleculares Aplicadas

2019-01-01 to 2019-12-31 | Contract
Fundação para a Ciência e a Tecnologia (Lisboa, PT)
GRANT_NUMBER:

UID/Multi/04378/2019
Source: check_circle
CIÊNCIAVITAE

The effect of enzyme flexibility on the catalytic mechanism of HIV-1 Protease

2014 to 2016 | Grant
Fundação para a Ciência e a Tecnologia (Lisboa, PT)
GRANT_NUMBER:

SFRH/BPD/94883/2013
Source: check_circle
CIÊNCIAVITAE

ENZYMATIC CATALYSIS - seeking a global picture

2013 to 2013 | Grant
Fundação para a Ciência e a Tecnologia (Lisboa, PT)
GRANT_NUMBER:

EXCL/QEQ-COM/0394/2012
Source: check_circle
CIÊNCIAVITAE

Strategic Project - LA 6 - 2011-2012

2011-01-01 to 2012-12-31 | Contract
Fundação para a Ciência e a Tecnologia (Lisboa, PT)
GRANT_NUMBER:

PEst-C/EQB/LA0006/2011
Source: check_circle
CIÊNCIAVITAE

Drug Design Targeted At HIV-1 Integrase

2009 to 2013 | Grant
Fundação para a Ciência e a Tecnologia (Lisboa, PT)
GRANT_NUMBER:

SFRH/BD/61549/2009
Source: check_circle
CIÊNCIAVITAE

Design de novos Fármacos dirigidos ao virus HIV-1

2008 to 2009 | Grant
Fundação para a Ciência e a Tecnologia (Lisboa, PT)
GRANT_NUMBER:

FCT PTDC/QUI/68302/2006
Source: check_circle
CIÊNCIAVITAE

Works (49)

Paradigms of convergent evolution in enzymes

The FEBS Journal
2025-02 | Journal article
DOI: 10.1111/febs.17332
Contributors: Ioannis G. Riziotis; Jenny C. Kafas; Gabriel Ong; Neera Borkakoti; António J. M. Ribeiro; Janet M. Thornton
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Crossref
grade
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Paradigms of convergent evolution in enzymes

2024-04-11 | Preprint
DOI: 10.1101/2024.04.08.588552
Contributors: Ioannis G. Riziotis; Jenny C. Kafas; Gabriel Ong; Neera Borkakoti; Antonio J.M. Ribeiro; Janet M. Thornton
Source: check_circle
Crossref

Enzyme function and evolution through the lens of bioinformatics

Biochemical Journal
2023-11-29 | Journal article
DOI: 10.1042/BCJ20220405
Contributors: Antonio J. M. Ribeiro; Ioannis G. Riziotis; Neera Borkakoti; Janet M. Thornton
Source: check_circle
Crossref
grade
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EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions

Nature Methods
2023-10 | Journal article
DOI: 10.1038/s41592-023-02006-7
Contributors: Antonio J. M. Ribeiro; Ioannis G. Riziotis; Jonathan D. Tyzack; Neera Borkakoti; Janet M. Thornton
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Crossref
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The 3D Modules of Enzyme Catalysis: Deconstructing Active Sites into Distinct Functional Entities

Journal of Molecular Biology
2023-10 | Journal article
DOI: 10.1016/j.jmb.2023.168254
Part of ISSN: 0022-2836
Contributors: Ioannis G. Riziotis; António J.M. Ribeiro; Nivedita Borkakoti; Janet M Thornton
Source: Self-asserted source
Antonio J M Ribeiro
grade
Preferred source (of 2)‎

The 3D modules of enzyme catalysis: deconstructing active sites into distinct functional entities

2023-06-05 | Preprint
DOI: 10.1101/2023.06.01.543252
Contributors: Ioannis G. Riziotis; António J. M. Ribeiro; Neera Borkakoti; Janet M. Thornton
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Crossref

Using mechanism similarity to understand enzyme evolution

Biophysical Reviews
2022-12 | Journal article
DOI: 10.1007/s12551-022-01022-9
Contributors: António J. M. Ribeiro; Ioannis G. Riziotis; Jonathan D. Tyzack; Neera Borkakoti; Janet M. Thornton
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Crossref
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The Enzyme Portal: an integrative tool for enzyme information and analysis

The FEBS Journal
2022-10 | Journal article
DOI: 10.1111/febs.16168
Contributors: Rossana Zaru; Joseph Onwubiko; Antonio J. M. Ribeiro; Keeva Cochrane; Jonathan D. Tyzack; Venkatesh Muthukrishnan; Lukas Pravda; Janet M. Thornton; Claire O’Donovan; Sameer Velanker et al.
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Crossref
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EzMechanism: An Automated Tool to Propose Catalytic Mechanisms of Enzyme Reactions

2022-09-06 | Preprint
DOI: 10.1101/2022.09.05.506575
Contributors: Antonio J. M. Ribeiro; Ioannis G. Riziotis; Jonathan D. Tyzack; Neera Borkakoti; Janet M. Thornton
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Crossref
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GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs

Nucleic Acids Research
2022-07-05 | Journal article
DOI: 10.1093/nar/gkac323
Contributors: Charles A Santana; Sandro C Izidoro; Raquel C de Melo-Minardi; Jonathan D Tyzack; António J M Ribeiro; Douglas E V Pires; Janet M Thornton; Sabrina de A. Silveira
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Conformational variation in enzyme catalysis: A structural study on catalytic residues

2021-12-13 | Preprint
DOI: 10.1101/2021.12.12.472283
Contributors: Ioannis G. Riziotis; António J. M. Ribeiro; Neera Borkakoti; Janet M. Thornton
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Crossref
grade
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GRaSP: a graph-based residue neighborhood strategy to predict binding sites

Bioinformatics
2020 | Journal article
DOI: 10.1093/bioinformatics/btaa805
Source: Self-asserted source
Antonio J M Ribeiro
grade
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PDBe-KB: a community-driven resource for structural and functional annotations

Nucleic Acids Research
2020 | Journal article
DOI: 10.1093/nar/gkz853
Source: Self-asserted source
Antonio J M Ribeiro
grade
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Identifying pseudoenzymes using functional annotation: pitfalls of common practice

The FEBS Journal
2020-10 | Journal article
DOI: 10.1111/febs.15142
Contributors: Antonio J. M. Ribeiro; Jonathan D. Tyzack; Neera Borkakoti; Janet M. Thornton
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Crossref
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A global analysis of function and conservation of catalytic residues in enzymes

Journal of Biological Chemistry
2020-01 | Journal article
DOI: 10.1074/jbc.REV119.006289
Contributors: António J.M. Ribeiro; Jonathan D. Tyzack; Neera Borkakoti; Gemma L. Holliday; Janet M. Thornton
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Crossref
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Exploring Chemical Biosynthetic Design Space with Transform-MinER.

ACS synthetic biology
2019-11 | Journal article
DOI: 10.1021/acssynbio.9b00105
PMID: 31647630
Contributors: Tyzack JD; Ribeiro AJM; Borkakoti N; Thornton JM
Source: Self-asserted source
Antonio J M Ribeiro via Europe PubMed Central
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Emerging concepts in pseudoenzyme classification, evolution, and signaling

Science Signaling
2019-08-13 | Journal article
DOI: 10.1126/scisignal.aat9797
Contributors: António J. M. Ribeiro; Sayoni Das; Natalie Dawson; Rossana Zaru; Sandra Orchard; Janet M. Thornton; Christine Orengo; Elton Zeqiraj; James M. Murphy; Patrick A. Eyers
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Crossref
grade
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Survey of the Enzyme Catalytic Residues in Mechanism and Catalytic Site Atlas

EMBL-EBI Research Retreat - 2019
2019-07-11 | Conference poster
SOURCE-WORK-ID:

cv-prod-id-2950738
Source: check_circle
CIÊNCIAVITAE

A Survey of Enzyme Chemistry

Encontro de Jovens Investigadores de Biologia Computacional Estrutural - 2018
2018-12-21 | Conference poster
SOURCE-WORK-ID:

cv-prod-id-2950709
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CIÊNCIAVITAE

Transform-MinER: transforming molecules in enzyme reactions.

Bioinformatics (Oxford, England)
2018-10 | Journal article
DOI: 10.1093/bioinformatics/bty394
PMID: 29762650
PMC: PMC6184704
Contributors: Tyzack JD; Ribeiro AJM; Borkakoti N; Thornton JM
Source: Self-asserted source
Antonio J M Ribeiro via Europe PubMed Central
grade
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Identifying pseudoenzymes using the Mechanism and Catalytic Site Atlas (M-CSA)

Pseudoenzymes 2018: From molecular mechanisms to cell biology, Sardinia, Italy.
2018-05-16 | Conference poster
SOURCE-WORK-ID:

cv-prod-id-2928662
Source: check_circle
CIÊNCIAVITAE

Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates.

Structure (London, England : 1993)
2018-03 | Journal article
DOI: 10.1016/j.str.2018.02.009
PMID: 29551288
PMC: PMC5890617
Contributors: Tyzack JD; Fernando L; Ribeiro AJM; Borkakoti N; Thornton JM
Source: Self-asserted source
Antonio J M Ribeiro via Europe PubMed Central
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Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites

Nucleic Acids Research
2018-01-04 | Journal article
DOI: 10.1093/nar/gkx1012
Contributors: António J M Ribeiro; Gemma L Holliday; Nicholas Furnham; Jonathan D Tyzack; Katherine Ferris; Janet M Thornton
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Crossref
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Benchmarking of density functionals for the kinetics and thermodynamics of the hydrolysis of glycosidic bonds catalyzed by glycosidases

International Journal of Quantum Chemistry
2017 | Journal article
DOI: 10.1002/qua.25409
WOSUID:

WOS:000406687800002
Contributors: Pereira, Andreia T.; Ribeiro, António J. M.; Fernandes, Pedro A.; Ramos, Maria J.
Source: Self-asserted source
Antonio J M Ribeiro via ResearcherID
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cuRRBS: simple and robust evaluation of enzyme combinations for reduced representation approaches.

Nucleic acids research
2017-11 | Journal article
DOI: 10.1093/nar/gkx814
PMID: 29036576
PMC: PMC5714207
Contributors: Martin-Herranz DE; Ribeiro AJM; Krueger F; Thornton JM; Reik W; Stubbs TM
Source: Self-asserted source
Antonio J M Ribeiro via Europe PubMed Central
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M-CSA Mechanism And Catalytic Site Atlas: A Database of Enzyme Mechanisms

EMBL Conference: Revolutions in Structural Biology: Celebrating the 100th Anniversary of Sir John Kendrew, Heidelberg, Germany
2017-11-16 | Conference poster
SOURCE-WORK-ID:

cv-prod-id-2928700
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CIÊNCIAVITAE

Redesign and Update of MACiE

EMBL Postdoc Retreat 2017, Alsace, France
2017-10-04 | Conference poster
SOURCE-WORK-ID:

cv-prod-id-2950463
Source: check_circle
CIÊNCIAVITAE

Redesign of MACiE: A database of enzyme mechanisms

American Chemical Society Fall 2017 - Chemistry's Impact on the Global Economy, Washington DC, USA.
2017-08-20 | Conference poster
SOURCE-WORK-ID:

cv-prod-id-2928763
Source: check_circle
CIÊNCIAVITAE

Unique Triphenylphosphonium Derivatives for Enhanced Mitochondrial Uptake and Photodynamic Therapy.

Bioconjugate chemistry
2017-02 | Journal article
DOI: 10.1021/acs.bioconjchem.6b00682
PMID: 28049291
Contributors: Hu Z; Sim Y; Kon OL; Ng WH; Ribeiro AJ; Ramos MJ; Fernandes PA; Ganguly R; Xing B; García F et al.
Source: Self-asserted source
Antonio J M Ribeiro via Europe PubMed Central
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Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms

Wiley Interdisciplinary Reviews: Computational Molecular Science
2016 | Journal article
DOI: 10.1002/wcms.1281
EID:

2-s2.0-84984706224
Contributors: Sousa, S.F.; Ribeiro, A.J.M.; Neves, R.P.P.; Brás, N.F.; Cerqueira, N.M.F.S.A.; Fernandes, P.A.; Ramos, M.J.
Source: Self-asserted source
Antonio J M Ribeiro via Scopus - Elsevier
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Binding free energy calculations on E-selectin complexes with sLe<sup>x</sup> oligosaccharide analogs

Chemical Biology and Drug Design
2016 | Journal article
DOI: 10.1111/cbdd.12837
EID:

2-s2.0-84988310710
Contributors: Barra, P.A.; Ribeiro, A.J.M.; Ramos, M.J.; Jiménez, V.A.; Alderete, J.B.; Fernandes, P.A.
Source: Self-asserted source
Antonio J M Ribeiro via Scopus - Elsevier
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Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD)

Journal of Physical Chemistry A
2016 | Journal article
DOI: 10.1021/acs.jpca.6b01536
EID:

2-s2.0-84978708569
Contributors: Sousa, S.F.; Sousa, J.F.M.; Barbosa, A.C.C.; Ferreira, C.E.; Neves, R.P.P.; Ribeiro, A.J.M.; Fernandes, P.A.; Ramos, M.J.
Source: Self-asserted source
Antonio J M Ribeiro via Scopus - Elsevier
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HMG-CoA Reductase inhibitors: an updated review of patents of novel compounds and formulations (2011-2015).

Expert opinion on therapeutic patents
2016-11 | Journal article
DOI: 10.1080/13543776.2016.1216977
PMID: 27537201
Contributors: Oliveira EF; Santos-Martins D; Ribeiro AM; Brás NF; Cerqueira NS; Sousa SF; Ramos MJ; Fernandes PA
Source: Self-asserted source
Antonio J M Ribeiro via Europe PubMed Central
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Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease

Acs Catalysis
2015 | Journal article
DOI: 10.1021/acscatal.5b00759
WOSUID:

WOS:000361089700073
Contributors: Ribeiro, Antonio J. M.; Santos-Martins, Diogo; Russo, Nino; Rarnos, Maria J.; Fernandes, Pedro A.
Source: Self-asserted source
Antonio J M Ribeiro via ResearcherID
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Insight into Enzymatic Nitrile Reduction: QM/MM Study of the Catalytic Mechanism of QueF Nitrile Reductase

Acs Catalysis
2015 | Journal article
DOI: 10.1021/acscatal.5b00528
WOSUID:

WOS:000355964300062
Contributors: Ribeiro, Antonio J. M.; Yang, Lifeng; Ramos, Maria J.; Fernandes, Pedro A.; Liang, Zhao-Xun; Hirao, Hajime
Source: Self-asserted source
Antonio J M Ribeiro via ResearcherID
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New insights in the catalytic mechanism of tyrosine ammonia-lyase given by QM/MM and QM cluster models

Archives of Biochemistry and Biophysics
2015 | Journal article
DOI: 10.1016/j.abb.2015.03.002
WOSUID:

WOS:000360781200012
Contributors: Pinto, Gaspar P.; Ribeiro, Antonio J. M.; Ramos, Maria J.; Fernandes, Pedro A.; Toscano, Marirosa; Russo, Nino
Source: Self-asserted source
Antonio J M Ribeiro via ResearcherID
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Synthesis and Hydrolytic Studies on the Air-Stable [(4-CN-PhO)(E)P(mu-(NBu)-Bu-t)](2) (E = O, S, and Se) Cyclodiphosphazanes

Inorganic Chemistry
2015 | Journal article
DOI: 10.1021/acs.inorgchem.5b00735
WOSUID:

WOS:000357705800044
Contributors: Shi, Yan X.; Liang, Rong Z.; Martin, Katherine A.; Weston, Nicholas; Gonzalez-Calera, Silvia; Ganguly, Rakesh; Li, Yongxin; Lu, Yunpeng; Ribeiro, Antonio J. M.; Ramos, Maria J. et al.
Source: Self-asserted source
Antonio J M Ribeiro via ResearcherID
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Analyses of cobalt-ligand and potassium-ligand bond lengths in metalloproteins: Trends and patterns

Journal of Molecular Modeling
2014 | Journal article
DOI: 10.1007/s00894-014-2271-z
EID:

2-s2.0-84901542884
Contributors: Brás, N.F.; Ribeiro, A.J.M.; Oliveira, M.; Paixão, N.M.; Tamames, J.A.; Fernandes, P.A.; Ramos, M.J.
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Antonio J M Ribeiro via Scopus - Elsevier
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Catalytic Mechanism of Retroviral Integrase for the Strand Transfer Reaction Explored by QM/MM Calculations

Journal of Chemical Theory and Computation
2014 | Journal article
DOI: 10.1021/ct500570g
WOSUID:

WOS:000346324000026
Contributors: Araujo, Ana R.; Ribeiro, Antonio J. M.; Fernandes, Pedro A.; Ramos, Maria J.
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Antonio J M Ribeiro via ResearcherID
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Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli

Acta Crystallographica Section D: Biological Crystallography
2014 | Journal article
DOI: 10.1107/S1399004714002570
EID:

2-s2.0-84900416783
Contributors: Hong, M.-K.; Ribeiro, A.J.M.; Kim, J.-K.; Ngo, H.-P.-T.; Kim, J.; Lee, C.H.; Ahn, Y.-J.; Fernandes, P.A.; Li, Q.; Ramos, M.J. et al.
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Antonio J M Ribeiro via Scopus - Elsevier
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A DFT study of the applicability of the charge balance model in two-metal enzymes: The case of cAMP-dependent protein kinase

Chemical Physics Letters
2013 | Journal article
DOI: 10.1016/j.cplett.2013.03.085
EID:

2-s2.0-84877833562
Contributors: Ribeiro, A.J.M.; Ramos, M.J.; Fernandes, P.A.; Russo, N.
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Antonio J M Ribeiro via Scopus - Elsevier
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Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes

Journal of Computational Chemistry
2013 | Journal article
DOI: 10.1002/jcc.23349
EID:

2-s2.0-84885957406
Contributors: Sousa, S.F.; Pinto, G.R.P.; Ribeiro, A.J.M.; Coimbra, J.T.S.; Fernandes, P.A.; Ramos, M.J.
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Antonio J M Ribeiro via Scopus - Elsevier
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Erratum: A DFT study of the applicability of the charge balance model in two-metal enzymes: The case of cAMP-dependent protein kinase (Chemical Physics Letters (2012) 51:49 12242-12245)

Chemical Physics Letters
2013 | Journal article
DOI: 10.1016/j.cplett.2013.06.024
EID:

2-s2.0-84880331802
Contributors: Ribeiro, A.J.M.; Ramos, M.J.; Fernandes, P.A.; Russo, N.
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Antonio J M Ribeiro via Scopus - Elsevier
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Protein-ligand docking in the new millennium - A retrospective of 10 years in the field

Current Medicinal Chemistry
2013 | Journal article
DOI: 10.2174/0929867311320180002
EID:

2-s2.0-84877933286
Contributors: Sousa, S.F.; Ribeiro, A.J.M.; Coimbra, J.T.S.; Neves, R.P.P.; Martins, S.A.; Moorthy, N.S.H.N.; Fernandes, P.A.; Ramos, M.J.
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Antonio J M Ribeiro via Scopus - Elsevier
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The catalytic mechanism of protein phosphatase 5 established by DFT calculations

Chemistry (Weinheim an der Bergstrasse, Germany)
2013 | Journal article
DOI: 10.1002/chem.201301565
EID:

2-s2.0-84928700256
Contributors: Ribeiro, A.J.; Alberto, M.E.; Ramos, M.J.; Fernandes, P.A.; Russo, N.
Source: Self-asserted source
Antonio J M Ribeiro via Scopus - Elsevier
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The catalytic mechanism of HIV-1 integrase for DNA 3′-end processing established by QM/MM calculations

Journal of the American Chemical Society
2012 | Journal article
DOI: 10.1021/ja304601k
EID:

2-s2.0-84865142881
Contributors: Ribeiro, A.J.M.; Ramos, M.J.; Fernandes, P.A.
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Antonio J M Ribeiro via Scopus - Elsevier
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Evaluation of DFT Functionals in the Context of the Hydrolysis of Phosphodiester Bonds

THEOBio 2011 - 5Th Theoretical Biophysics International Symposium
2011 | Conference poster
SOURCE-WORK-ID:

cv-prod-id-2950143
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CIÊNCIAVITAE

Benchmarking of DFT functionals for the hydrolysis of phosphodiester bonds

Journal of Chemical Theory and Computation
2010 | Journal article
DOI: 10.1021/ct900649e
EID:

2-s2.0-77955561344
Contributors: Ribeiro, A.J.M.; Ramos, M.J.; Fernandes, P.A.
Source: Self-asserted source
Antonio J M Ribeiro via Scopus - Elsevier
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Recent advances on computational proteomics

World Academy of Science, Engineering and Technology
2009 | Journal article
Part of ISSN: 2010-376X
AUTHENTICUSID: P-007-X1N
EID:

2-s2.0-78651571830
Contributors: Sousa, SF; Cerqueira, NMFSA; Perez, MAS; Moreira, IS; Ribeiro, AJM; Neves, ARAP; Ramos, MJ; Fernandes, PA
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Authenticus

Peer review (7 reviews for 5 publications/grants)

Review activity for Communications biology. (1)
Review activity for Genomics, Proteomics & Bioinformatics. (2)
Review activity for Journal of chemical information and modeling. (2)
Review activity for Molecular pharmaceutics. (1)
Review activity for Topics in catalysis. (1)
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